I greatly agree with Joshua's answer, but I feel he's taking some shortcuts in his understanding of the player you have a problem with. It is not so much that he likes idealized stories, whilst you like realistic stories. For one, people do change, and with effort a lot of people can be convinced, so from that perspective scripted stories are the unrealistic ones, whereas his best effort attempts are the realistic ones.
Either way, to get to the point, the best solution I can think of in your case is to give him what he wants whilst you still have your stories to build the way you want them. How? Simply by presenting characters he can 'save' whilst you still have your 'evil villains' that propel your story forward. The trick is to design characters that 'by the script' all can be 'converted', however where it depends a lot on who they are whether achieving that is realistic. So, lets first examine what factors influence one's ability to convince someone:
- Age, out of all factors I believe this is the most important one. It's a hard lesson I had to learn in real life as well, but the older someone is, the stronger they stand in their convictions. It's not even because they have the experience to back their positions, it's simply a part of human nature.
- Psychological state, are they even capable of rational thought. In most cases they should be, but some can be literally crazy, or somehow affected or controlled by other beings.
- Knowing their Agenda, why is the villain doing what he does? In a well designed campaign they always have their reasons (except in cases where they are unable of rational thought), so without knowing those reasons 'saving' them is impossible.
- Model of Morality, a common motivator of villains is the well being of the majority. For example "it's fine to run experiments on an entire village that cost their lives if that allows me to save/improve the lives of thousands of others". If the player in question follows a different moral model, then no matter any convincing he will do, the villain in question will never be convinced.
- Revenge or other similar motivators are closely related to the above, though not always clearly so. If you believe it actually morally right to genocide a certain people, because they killed your parents or your lover, then no matter how much convincing you try to do, you won't succeed. At best you might convince them to kill less people.
Now, based on those kind of things you could model a group where this player has a chance to 'save' a lot of (in the grander scheme of the story) inconsequential people, yet still saves the lives of many. For example, the villain could have a young student (or even his own son) who is also his right hand man. As he's young and doesn't truly share the agenda of his 'master' convincing him should be quite possible, however spending so much time convincing him gave the master enough time to plan for it. Well, that's the cliche version at least, there's a lot of ways you can go with this. One thing to look out for though is that the 'main' villain never can be convinced, instead it could also be that 'main villain' is a young guy that can be convinced, but after convincing him somebody just jumps into his place. Either way, jumping back a bit, teaching the player that spending a lot of time on such actions can come at a cost will allow you some control over how much time the player spends on these kind of things which you should base on how the rest of the group takes it. If they enjoy listening to him solving their problems in creative ways: Good, and otherwise just put some healthy indirect time pressure on him.
Oh well, as a final conclusion I can just say that I do not think it's hard to give such a player enough room without compromising your stories, so I see no reason for some of the drastic measure suggested by Joshua's answer or focused conversations like suggested by Tritium (mind you, such a conversation is great when done naturally, but the way I imagine Tritium's advice being acted out it could backfire by putting too much focus on his play style in a negative light). I mean, that advice would be great if the problem would be huge, but honestly, what you're dealing with shouldn't be that difficult to handle by a bit of creative story planning.