When you roll up a character, you decide what it's morality is. Either you will be a "good" character, you will be an "evil" character, or you will be a "neutral" character.

To say a paladin who devotes his life to stamping out evil in all it's forms shouldn't kill you just because you have a red aura is stupid. You ARE evil. If you aren't acting evil, then you aren't RPing properly. That's your fault, not his.
Similarly, if you've chosen a good alignment, then you ARE good. So act like it. If you don't want to act good or evil, then choose neutral. It isn't that complicated of an issue.

Now, think in practicality. You have to have a reason a "good" person would kill another "good" person.
They're destroying the forest, and you like the forest? Fine. But Warders already do that.
They're using magic, and you hate magic? Fine. But Villagers already do that.

Can you think of a reason a goodie sylvan would kill a goodie maran paladin? No. Well, neither can that sylvan. So he doesn't do it.

By definition, a "good" character will not go around murdering people without good cause. If they did murder people just for the hell of it, well.. that wouldn't be very good, would it?