Everything he says or does seems to be for the human race. He is fighting the angels who have had a majority vote to kill us. He told us our allies were merely controlling us. He told us to run from our allies, and then we just jump and kill him. Why?
He just seems misguided. He's a well intentioned extremist.
Zoltun's story is rather interesting, to say the least. He presented himself as being in support of the human race, but this support was somewhat disingenuous, as he also craved power. Lots of power.
As the story unfolds, he then calls for you to abandon everyone else in order to bring him to ultimate power. Not only would you enslave yourself to him, this would also go against everything you, Tyrael, and Leah have been fighting to restore.
Everything you say is so absolute, but almost none of it is actually conveyed in the game. When does he tell you to abandon everyone? Why would keeping him alive enslave you? The only thing that happens before you fight him is his stating of something being wrong with the blackstone and to not trust the ones close to you. It's almost like you guys played a different game then us.