Well, if you change something into a corpse, you don't commit murder unless the thing was alive in the first place.
Even if you cast the Stone to Flesh spell upon a statue that was alive in the first place and you fail to revive the creature (because its Fortitude save fails), this still doesn't mean that you killed the creature, only that you tried to revive it and failed.
And if you change a statue that was never a living thing into a corpse, you don't murder anything, because the statue never had a soul.
Finally, if you change a stone golem into a flesh golem (as mentioned in the description of the Flesh to Stone spell), you only change the container that holds the golem's soul, which is probably some kind of elemental spirit. Even if you think there's something Evil about imprisoning the elemental spirit in the first place (and I have argued earlier on this thread that there isn't anything Evil about this), there's probably nothing Evil about changing the substance of its prison from stone to flesh.
So changing something into a corpse doesn't seem to me to be morally the same as changing a corpse into an undead.
Once you have a corpse to work with, you can either animate it as an undead or animate it as a flesh golem. In the former case, you create a creature whose default nature is Evil, whereas in the latter case, you create a creature whose default nature is Neutral, so there's still a moral difference there.