The last point is a bit pithy but also relevant. If your players are checking for evil and killing npcs, maybe they are really calling for a nice simple bash evil and have fun type of game. You have give them what they want or they will certainly act up. Good luck.
Pretty much this in a nutshell. Bob detected as evil -- so what? That doesn't give you the right to run up and kill them, be you a paladin or policeman or cleric or whatever. If that is the main issue you are running into, it isn't the alignment system that is a problem.
A shades of grey world won't change player behavior. Removing alignment doesn't make people role play in a less disruptive way if that is their thing. Much like everything in the rules, alignment is part of the tool box, and like everything there, if it doesn't work for your game you can remove it. But I don't see them removing it from the game as a whole, anymore than removing guns, ninjas, puppies, or whatever it is that bugs certain groups would solve anything.
Make the game your own by customizing.