I do not agree with the flesh golem. It can go berserk in which it destroys what is nearest, including any sentient beings. If you except that that is not evil and is okay then how is a zombie or skeletons potential actions any different?

I know the RAW answer is because a developer wrote it so, or it's another sacred cow that wont die. A N entity can do evil acts, anyone can, but it is lacking in the capacity to differentiate. Animals consume to survive because of instinct, are undead (non intelligent) likewise motivated by instinct? I agree it doesnt make sense and is unsatisfactory and I dislike that even though I am certain the answer is actually cause developer X thought so without a lot of thought, like nearly every alignment based thing in 3.5. See also sanctify the wicked dominate person etc.