referencing it (or even lifting it in this instance) =/= respecting it, necessarily.
I think in this case, it did, because the one thing that Bendis did that was really cute was have the dialogue that he absolutely should've: He had Hank Pym realize that he was building a sentient robot that would continue to evolve and grow increasingly dangerous.
That was the part about respecting Marvel history that I'm truly referring to: The whole point of this story, the whole point of this ENTIRE story, isn't that we didn't see Ultron.
The whole point is that at some point, Ultron was going to kill us all. Yesterday, today, tomorrow, Ultron was going to kill us all. That paradigm had to be fixed -- at some point, "Age of Ultron" was going to take place, and Hank Pym was responsible for it.
Bendis didn't invalidate any of the stories that came before him. He took the stories to their logical conclusion, and by doing so, gave one of Marvel's longstanding heroes a chance to right one of the single-biggest tactical errors ever made.