This old problem.
The issue here is importing our modern, complicated notions of the words "Good" and "Evil" into a world where morality is a fully realized, divine or semi-divine force. In our world, good and evil are debatable. In Pathfinder, Good and Evil define your character in an objective sense.
You can certainly play DnD/Pathfinder "straight," which means you accept the moral precepts it lays down. Some creatures are, in fact, evil. Evil should be destroyed. This allows you to go about your campaign without wondering about these moral quandries. You kill evil things and take their stuff. A horrible way to exist in our world, certainly, but in Pathfinder, that makes you a hero, because evil is bad.
If you want to discard that notion entirely, and treat alignment as a moral code you aspire to (like in our world) rather than an inherent force that places a mark on your soul, go for it. If you enjoy the kind of dilemma you are facing right now, then by all means import all the moral/ethical BS from our world.
The important thing is you agree with the table about which version of the game you are playing. Never cross the streams. If the Paladin is going hardcore Gygaxian, vaguely racist genocide, and the Wizard is planning on clucking his tongue and demanding that the DM have him fall every five minutes nobody is going to have fun.
So, take five minutes before your next session and ask, OC, which kind of Pathfinder you want to play. Maybe your DM should just lay down the law on what good and evil mean, and go from there.