Re: Players forcing my hand
There are really only two options:
1) Get new players. I mean, really. That sounds harsh, but it's true. Ultimately, you can't have a group where one guy wants to play a villainous scumbag and one guy wants to play Dudley Do-Right and still expect to be able to run a game where everyone can have fun. Although a good campaign is flexible enough to accomodate many different philosophies of play and role-playing aims, ultimately, there is a point past which all members of the group have to be on basically the same page.
Try talking to these players before taking any drastic action, of course. I think problems like this are metagame issues and best approached that way. The choice to play a killer or a non-killer in a supergame is a matter of the "feel" of the game more than anything, and that is something to be hashed out between the players and the GM, not within the campaign world. In the final analysis, in every game the players do or do not do things not because they make sense internally, but because they are genre-appropriate. Superheroes wear bright spandex not because it makes sense necessarily, or is the most pragmatic thing to do, but because it's in genre. If you don't think that the PCs offing your villains is a good thing for everyone's enjoyment of the game (including yours! you may be GM, but you are there to have fun, too), tell them so, and tell them that they are disrupting everyone else's fun. This isn't an issue of one CHARACTER aggravating another, it's an issue of a real person stepping on the toes of one or more other real people, and that's something that should be handled by the real people involved.
2) Failing a metagame solution, I can only recommend loosing the fires of Hell upon them. I mean, don't get malicious, or they will be deservedly bitter. But killing NPCs is not acceptable in most superhero worlds, and will generate a s**tstorm for the PCs in question. Aside from average citizens being afraid of them, other heroes will be out to get them, friends of the villains killed, other villains who think they need to off the hero first, etc etc. The more people they kill, the bigger this will get, until it consumes the entire game. And don't be afraid of that. In a sense, this is a metagame solution, too, because unless the players of these characters enjoy spending ALL of their playing time in a constant running battle with police, UNTIL, the FBI, PRIMUS, other heroes, and a whole cadre of villains, then they will eventually get tired of it all, and decide to quit killing NPCs just because it's less hassle to let them live.
Important note. Ask yourself if the PCs have a REASON for this behavior. If you've constantly emphasized the "revolving door" view of putting super criminals in jail, then I can't say as I totally blame them for their tactics. Remember, players tend to act toward their own interests - you can't run a swashbuckling game where people swing from chandeliers regularly if you try to get all detailed and picky about the amount of weight chandeliers will support and so on. In short, if you've been leaving these players with no viable options for stopping these villains from running amok, then the fault lies in yourself, not in your stars, so to speak. However, if they are just bloodthirsty, see above.