Have you ever read Order of the Stick? I see that KRyan's used it in his answer, but it's a good example. However, in my games, I've used three different methods that work pretty well.
Don't get me wrong, I'm all for letting players choose their character roles and archetypes, in fact I think it's the best thing you can do to facilitate a good gaming experience. However, characters are a product of group consent even if they are individually created by each player. If the party has characters who absolutely will fight all the time without stopping, you need to just let them work out the violence. This requires players who are mature enough to be allowed to do such a thing, but I've never seen this turn into too much of a problem, both as a GM and a player in this situation.
Basically, let the players work out the direction in which they want to take the group by allowing them to fight and imposing consequences on individuals or the group as a whole as a result of the repercussions of their actions. This doesn't "answer" your question, but I think that you may be more concerned about this than is necessary.
"Everyone is the good guy in their own head." Consider that when you're dealing with an evil character in your games. If you're looking at a truly psychopathic chaotic evil murder machine, you may actually want to forbid the character because they're a disruption to play. However, I've found that there can be groups with alternatively aligned political extremists; any Shadowrun game I've run has an example of characters who clash from a variety of sources, but the truth is that at the end of the day they're working together for a common goal. Even if it's personal gain, they've realized that their best opportunity is to just work together in order to keep the group intact so that they can get an optimal return on the profits.
Another thing to consider is that the betrayal underlying the group's foundations can actually be a bond; they have to give each other signs of trust, and should both sides prove to be responsible they will then have a character relationship that transcends their alignments.
Evil vs. Amoral
Running with the last concept, consider whether characters are supposed to be "evil" or just have no qualms with doing harm. For instance, Rorschach from Watchmen. Many characters are willing to do horrible things either for a perception of greater good or just an apathy for the general condition of mankind, but will not actually cause harm unprovoked. For instance, these characters will take out a guard by slitting his throat instead of knocking him unconscious (the medically dubious nature of reliably rendering someone unconscious aside), on account of the fact that it's a more certain solution. While we're on the topic of comics, The Punisher presents a protagonist who is very good at this. The secret to creating an evil aligned character who is more than just an alignment label is that they are opposed to something, not that they're opposed to everything.
Encourage players to break alignment. It's very hard to have a good, deep character using some of the alignments because they just aren't built to create deep characters; they're meant to create easy to roleplay characters. They're a general description, not the list of personal values and motivations.
List motivations. Eclipse Phase integrates this very well; a character may be +Anarchism and +Populism, and -Violence. Evil characters should have positive motivations, and shouldn't just be +Violence, +"Bad Things", -"Good Things". If your system has an Edge/Action Point/Moxie/Bennie system use the motivations to determine how they are earned.
Encourage evil to manifest in ways other than violence. It's okay to have a rapacious magnificent scheming evil villain as a character, but it's typically not a good idea to have evil characters who look more like the Psycho from Borderlands 2 than Hannibal Lector. Likewise, not every Malkavian is going to check the flavor of the nearest wall every fifteen seconds.
Good and evil is not always clear. Sometimes the good guys manage to cause massive harm by doing what they think is right, and sometimes those who don't care about the impacts their actions may have on others don't actually wind up harming those around them. Good guys who let a villain go may wind up allowing them to cause massive destruction, and bad guys who take down a supposed paragon of good may discover that their target was just as flawed as they are.
Give players obligations and encourage them to share character histories; they should have reasons not to attack each other if they're traveling partners, business partners, or the like. Their honor or reputation may be on the line, and it may be impractical for the good guys to take down the evil guys in the party just because then they wouldn't be able to keep doing as much good as they do.
Encourage evil characters to be passive. It's not necessary for evil characters to always run in and smash all the good characters' work "for the 'lol's", instead it should be a premeditated, scheming, "What do I get?" situation where the evil characters work with the good guys for the wrong reasons but wind up doing good. Jayne from Firefly looks like this at times, even though he's probably not.
Encourage good characters to be passive. Sure they're with a band of ravaging, bloodthirsty psychopaths, but so is everyone else. They can't change the way the world works, and if you're in a Game of Thrones style world then they'll be a solitary glimpse of light amidst a dark abyss of moral decay. They have to pick their battles, and this isn't it.