So if you want to put a little morality back into the game, award bonus XP for not killing people, award bonus XP for taking the bad guys to jail, award bonus XP for working in a heroic, moral fashion.
Yup. Of course in a Machiavellian campaign you could give XP for being clever and ruthless, in an Evil campaign you could give XP for being Evil in accordance to your campaign's genre norms - you don't sacrifice the princess to the Dark Gods in a Disney-themed campaign, but you might give her a poisoned apple that sends her to sleep for a hundred years.