tl;dr When life presents you with lemons, make lemonade
All of the things you mentioned can be worked into the game to make it a be tter game. That's what makes role playing feel alive and appealing. Try to find a way to incorporate those things; turn the problems into flavor.
Railroading is a valid game style, and some players even prefer it for various reasons, but that should be the exception not the rule. It doesn't sound like that's the case with your players.
I have edited this section since OP let us know that yes, the necromancy tome would unbalance their world and make it broken-powerful. See also this question about how to deal with a game where you accidentally allowed the players to acquire something that breaks the balance for them.
What is the real problem?
You did not say necromancer players would be difficult to allow in your setting and would make play impossible, so I'm going with the assumption that you just don't want it. The only reason I can think of to specifically disallow a necromancer is because having a mob of skeletons or zombies around you would be difficult to explain to the town guard.
Other than that, the rest of the abilities aren't as much of an issue.
"Wow, you beat that goblin good; what was that technique?"
"Oh, just a battle spell I picked up along the way."
And what about when interacting with the dead? That's just flavor right there, especially if the player needs to try to do it discretely.
I have both DM'ed games with necromancers and I have played a necromancer. Sometimes the necromancers are not truly evil, but their moral standards are just sub-par. Think of grave-robbers, trying to benefit from the corpses in the graveyard because they are easy targets; a neutral necromancer could have the same mentality.
And for the first point, about the "I want to release the world-destroying evil," that one sounds like a dork move on the player's part, but it should not ruin the campaign. If it took a team of heroes a campaign of adventure to keep the evil from releasing, how is it so easy for this 1 player's character? Your vote to "allow" I assume means "Do you want to tell Bob he can't do that?" (that is, out-of-character).
In character, the rest of the party is likely to save the world again, from their own member; that's an interesting game right there. I have been part of games like that, and it adds flavor.
All these "problems" add flavor
More on necromancers... because they are cool (in games, anyway)
When you need to be discrete about your necromantic tendencies, sometimes it gets interesting. I once had to take only a small portion of my undead mob with me, only as many as I could cast disguise spells on and pass off as living to the commoner NPCs. Having a bunch of undead minions was necessary for what was going on as we needed many hands, yet we had to get by without having the town folk pitchfork us.
Also, having fewer undead in number that are higher level makes it easier at times. But sometimes it is just way cool to unleash a horde of minions, even if they are weak.
And back to the "Literally destroy everything by unleashing powerful evil"
I have DM'ed games with evil characters before, though none where they wanted to destroy everything. Even if you failed to stop the player from succeeding, there are still ways you can save your world.
Maybe the power being unleashed is not so powerful that it can
destroy the world instantly and there is time to try and find a way
to stop it. (How was the evil locked up in the first place? Do that
Maybe the knowledge about what would happen if this evil were
unleashed was not completely accurate (even if the evil entity
itself said some of the things).
As a DM you need to metaphorically make a dodge roll so your world can take half-damage.*
Characters like lots of power too
I once DM'ed an adventure where the party went to a disaster zone to help people and to secure some magic that evil forces wanted. Among the ancient treasures that needed to be kept away from the evil forces was one major artifact that was powerful beyond the others. I knew the players and the characters well and trusted them to handle it accordingly.
The party did indeed save the day, beat the enemies, and acquire the powerful items. I assumed they would give the major artifact to one of the available magic organizations that could protect it, as it was a dangerous item the kind most sane people would not want to have in their possession. But one player character, a sorcerer, was so drawn to its power that he wanted it for himself.
In the final encounter the sorcerer teleported past the fight when just before it finished and took the artifact. There was little the rest of the party could do to stop him, as the sorcerer had more spell power left than the others. In the end, the rest of the party convinced him to let it go, that it was not safe. They all agreed that it needed to be destroyed completely, so that is what they did.
One player told me later on that that was the best adventure that he had ever played, for multiple reasons, the realistic party dynamics among them.
Now, even if the sorcerer had managed to take off with the major artifact, that still would not have ruined the game. This was a large game that two of us were DM'ing together, a vast, living world with dozens of player characters in it ranging from 1st level to epic level characters. The sorcerer was high level, so having a major artifact would have increased his power probably by 2 or 3 times but not broken the character.
During the dialog between the party members in the tense moments before the sorcerer gave in, I was seriously intrigued by the ramifications of him running away with the artifact. Even though the sorcerer could have been a few times more powerful with the artifact, it would have cut him off from the rest of his party, making him a party of 1 character that was effectively less powerful than the complete party he was with before.
Although I think it would have been fun to deal with the sorcerer had he left the group, I do admit there are plenty of facets to consider. Does this mean the game you are running gets split into two games? For the world I was DM'ing, that would not have been an issue since there were already multiple separate parties of characters which were changing and evolving over time anyway as characters shifted between adventures and parties. You need to answer that for your group.
For the normal campaign, this would be more difficult, but not without options. Could you separate a bad apple from the group and make that character a new villain? The DM does not always need to be in charge of the villains. This is my first choice in this situation. If you do this, you do not necessarily need to get rid of the previous villain(s) (assuming they haven't already been defeated by the party before this problem arises); there can be multiple villains, and villains can even be at odds with each other, or they can be allies.
Imagine a game where you do not need to set up the traps and enemy placements on your map because you have someone to do it for you? You generate the level appropriate list and just hand it to the player-turned-enemy to populate the map with them because he's in charge of it.
You could even let him control the enemy mini-bosses, or even all of the enemies if you wanted. Then you can concentrate on other DM tasks more. In this situation, the enemy player must understand fully ahead of time that the odds are being stacked slightly against the enemies, so that the enemy player's forces will likely be defeated; the player has to be OK with this.
If you don't mind splitting the game up into two sub-games, that works too. The point is, there are options. Even for the dork-move where your player wanted to unleash the world-destroying evil, there are still options.
RP DM'ing is not a "DM vs players" thing, however, the DM is controlling the world and so sometimes needs to be the world's player to save it and be crafty and scheming for it the same way the players are for their characters.
Sometimes saying "No" is necessary, like when you get the new player who you thought you were being nice to by letting him start at level 3 to match the existing players, and he responds with "And my guy is the son of the king and rides a huge fire breathing dragon!" Generally though, as long as the players are being reasonable, trying to work around the player's ambitions and fun is more interesting for everyone, and more fun for the players, than simply saying "No." And it sounds like your players were being reasonable, with the possible exception of "I suddenly do a 180 and want to unleash the world-destroying evil," though even that can be fun to incorporate.
If you cannot think of what those options are right at that moment in the game, sometimes you need to take a break. If you've been playing a while that day, call it the end of that session, even if it's early. If not, at least take a short break for restroom use, or for snacks, or whatever, just enough to give you 5 or 10 minutes to find your world's escape route.
Here are a some ideas for your first and third examples:
"I want to unleash the power that destroys the world."
Ok, go ahead. Oh wait, another party of heroes (NPCs) just walked in
the door after you "saved the day" but changed your mind. They were on
a similar quest as you but just a step behind. Now they are saving the
world from you.
Yes, the previous one is a bit lame. Let's do a better one...
The evil force awakens, and the forces that held it captive all this
time slowly fade. The dark being takes notice of this too and is
enraged that its freedom is not immediate. It appears that the release
will take some time.
And then you could have it take days, weeks, even months of in-game time. Or speed up the release but say that the entity does not yet possess its full power, so it can still be stopped. This leaves another session for the players (minus the dork who sacrificed their self to release the evil) to deal with it later.
For the necromantic tome, if it is so over-powering then that means others will want it to. Once word gets out that this player has it, suddenly the party will be on the defensive instead of the offensive. That player character is likely to be besieged by many creatures more powerful than their self, creatures they did not even know existed before.
Or the tome could have negative affects. It can be as simple as "the negative energy of the tome causes you to lose 2 levels," or it can be more intricate like every time the tome is used it attracts dark-energy monsters who attack its user - what a nuisance! Or maybe it constantly drains the user's energy while in use, so although it is overpowering it can only be called on sparingly without killing its user.
If you simply cannot come up with any ideas on how to allow something in your game, and it would break your game, then you can always fall back on "Hey guys, I simply cannot figure out how to work this into the game, and I think the game would break. As much as I want to respect your characters, I just don't think I can make the world work after that change. Could we step away from that just so we don't have to lose our game?" But that should be a last resort. If it does come to that, the voting (which you already did) is a good addition.