What are you basing this on?
Alignment - Pathfinder_OGC
But I mean, I could just ask you. Is it good or evil to kill an innocent man? If you look at the description of Good vs. Evil in the link I posted, you will see that the answer to this question is not, "It depends." The description contains no "maybes"; no grey areas. No talk of thoughts; only talk of deeds. Further, an objective moral standard has been a part of D&D since time immemorial - devils are LE, demons are CE, etc. This distinction is based upon the acts of the creatures in discussion and the requirements for a certain alignment. The man who thinks he's killing demons is not good-aligned if what he's really killing are babies, despite his good intentions. Intention does not alignment make - only deed.
As a final point, and this is probably the most important point to make, here is a quote from the sidebar of the GameMastery Guide in that same link I posted above:
"...there exist creatures in the Pathfinder Roleplaying Game that are fundamentally good, evil, lawful, or chaotic..."
How would this be possible if there were not a fundamental, over-arching,
objective moral standard? If the Pathfinder roleplaying game considered morality to be subjective, this fundamental distinction would not be possible. I said essentially the same thing when I mentioned how demons and devils with their respective alignments have been in D&D for a long time. This just says it more clearly.
Man, I'm just FULL of good points today! Here's another one:
If you read the description of the Paladin class you will see a section on ex-Paladins. This includes a link to the Atonement spell.
http://www.d20pfsrd.com/magic/all-spells/a/atonement
In this description, you will see the following:
"If the atoning creature committed the evil act unwittingly..., atonement operates normally at no cost to you. However, in the case of a creature atoning for deliberate misdeeds, you must intercede with your deity (requiring you to expend 2,500 gp in rare incense and offerings)."
The word "unwittingly" implies that a character may commit an evil act without knowing that he is doing it, and this act is still considered evil and would require an atonement spell for a class like a Paladin. This would fit with your example of the guy who thinks the baker is an evil necromancer and murders him in the name of good, only to find out later that this act was an evil act (despite what the character thought at the time).
This is just another example of how "belief" means nothing because there
is an objective standard that judges each character based on the actual acts committed. Did the PC kill someone innocent? Did the PC save a town from death? Did the PC catch evil demons? There is no room here for, "how does the PC feel about what he did?"