Polymorph any object and souls

[Xefas]

I think a human created from an inanimate object would keep its original mental abilities. in other words, become comatose.

That would be a houserule, considering:

Unlike polymorph, polymorph any object does grant the creature the Intelligence score of its new form. If the original form didn’t have a Wisdom or Charisma score, it gains those scores as appropriate for the new form.

Does he die at the end of his 3 hours? Is it murder?

On the subject of morality, I don't think an artificial human's lifespan running out counts as murder any more than a mother becomes a murderer for their child dying of old age.