There's a difference between 'I worship X' and 'I am empowered to do magic tricks by the magical might gifted to me by X and the clergy that directly communes to and espouses their message.'
It's kinda like the difference between being a Cristian, and being St. Paul, or Elijah, or Abraham, or any other prophet or holy man. Not every adherant to a religion necessarily walks the straight and narrow of that belief system. There are some who murder when thou shalt not murder, or steal when thou shalt not steal.
However, when the diety starts handing out the hocus pocus, that stuff's only going to those who actually got their head on straight (by the diety's point of view.)
You might have a lawful good person who worships the Raven Queen, believing that his hunting of vampires is for the common good. He believes he is doing the right thing, and that everyone should do the right thing.
However, The Raven Queen isn't doing it for the common good, she's doing it because fate must not be abated, good or evil... the deathless are as culpable as the undead. But those chosen by her? They're fated to be that way, so do not defy her will, whether they do evil or good. Thus, one entrusted as her cleric, or paladin, would be unaligned. Her clergy doesn't hand that stuff out to shining white knights who don't quite toe the party line.
