So, was the AI Will or not?

I got confused. As the movie progresses ppl move to considering that the AI isn't him and it's turning ppl into minions. But then in the end Evelyn is uploaded and says it was him all the time, and that he was healing the world! And that he never wished to change the world, but he was doing that because it was her wish.

Either way, he was taking control of ppl he healed. Sure he didn't kill them, but I can't see how it couldn't be wrong to take control of them.