The bit at the end was interesting, saying he would never doubt her. Makes you wonder if they made a mistake, which, is very, very likely. Or, more likely, they dont care about any of the other established stories (other than the Saga). Obi-Wan has suspected (or known) for awhile about Anakin and Padme. The smirk and raising of the eyebrow said it all. I like how they alluded to Anakin's deceit in Episode III. His fear of loss controls his every action, and it is very evident in this episode.
Lucas did say that he ignores the novels in general because "they have their world and I have mine," or something like that. Although I am curious what other novels/comics has Anakin hinting that he doubts Padme? Because even w/out the novels/comics (if there are any) his doubt is shown in EpIII--but I suppose Palpatine had a great hand in having Anakin doubt her. Obi-Wan knowing about them, or having a clue about them makes sense. He wasn't surprised at all to find out that Padme was carrying Anakin's children. In fact, he went to her first when he was looking for him. It would have really helped us if they didn't delete some scenes concerning Obi-Wan, Padme, and Anakin in EpIII. And like Brodoin and Zepherous said, it's nice to see how attached Anakin is because it is the cause of his downfall.