Does anybody outside of Avengers Tower even know that Tony is the one who created him?
No, but I think he meant that it was weird that everyone was still all buddy buddy with Stark after they defeated Ultron. He still went behind the team's back and caused the problem in the first place. At least Banner admitted he was wrong at creating Ultron at some point.
I mean, them defeating Ultron shouldn't suddenly mean that Thor doesn't want to wrap his hands around Stark's neck anymore for causing the problem in the first place.
But they can't do that here, since none of the MCU heroes have secret identities. They're all public
Well the secret identities thing is out the window, but there is still the issue of accountability. Unless I've missed something from the lead up to this movie I don't think that they're going to make it to where registering with the Government leads to the Avengers being Government lackeys. At least I hope not, because that doesn't seem like something Stark would support anyway
The comic and MCU versions of Civil War are based around different concepts. The comics are about registration, but the MCU version of Civil War is based around wether superheroes should be controlled by the government.
EDIT: Beaten to it.
Oh, I guess I did miss something. That seems like a bad way to go about it. As guilt stricken as Tony is about everything it still seems very out of character for him to support the Government telling the Avengers what they can and can't do to save the world.