The Marvel film-verse (including Hulk, Captain America, Thor, & Iron Man movies) has its own canon, separate from the comics.
So the easy answer to your question is "Yes, this is canon for the films," as the film itself is a canonical source.
Outside of that, I believe Tony Stark has gone through many ups and downs in his life in the comics. Simply destroying the armors and the reactor won't stop him from creating new armor or new reactors in the future.
What I think you're missing is that Tony Stark is making a point - HE is Iron Man. The armor doesn't make him a hero, it's just a tool. He's making the same point that he and Rhodie made in Iron Man 2 - it's the person inside the armor that matters, not the armor.