Hm... I never felt that twist because the "happy ending" of the second movie never seamed realistic anyway.
So they blew up a couple computers and melted the scrap terminator parts. The lead scientist is dead. All good now. Whaaat?! There is an entire research team around the guy, that is still alive. They may not be as genious and they don't have the parts anymore. But they have seen them. They know it can be done. Their bosses know it can be done.
The office building will be replaced by insurance. If not, they will just raise money. If they can't, the research team will be taken in by some other tech company, that has enough money.
So the theme of the movie was actually misleading. They never prevented anything, they just postponed it. The Connors were lying to themselves. As for the terminator, maybe he was programmed to believe it/to lie about to make sure they don't lose faith. Maybe he was sure other humans would be too stupid to finish the research. Thinking to binary ;D
I think it was more of an open-ended ending