Then as a back-up, he just has contingency plans or he just starts gathering others weaknesses which Ultron eventually gets a hold of. The plan could include a cyborg Thor clone.
The Shield fallout can be big enough, I mean it targeted and tried to kill him and it was an organization he already did not fully trust. After Shield turned out to be Hydra he could be "I knew it" or "told you so".
I mean him building robots to take over what Shield was doing, protecting or whatever, is in a way a sort of paranoia? Or arrogance? Whichever.
As for the registration act, I think all these events will play a part in the Civil War too including Shields fallout. He could side with it just so there are no surprises like Hydra, I mean that was one of the things they touched up on in Cap, revealing peoples/agents secrets. Stark could believe that secrecy leads to betrayal or surprised evil or whatever.
He was also arguing with Fury in Avengers about the secrets like secretly using the Tesseract power to make weapons. He was already hacking and exposing their secrets. The event of Cap2 and Ultron going haywire (or if for some reason Hydra has something to do with Ultron going nuts, it does look like he is working with the twins and last we saw, the twins were with Hydra -or being experimented on by Hydra- so there could be a connection there) could push him over the edge and might even start the registration act?
I don't know, just some late night pondering.