I fully agree with you. There's really a ton of ways they can re arrange the arcs from ASOS/AFFC/ADWD, including quite a few possibilities that could make it better in the context of a TV series. Some of those choices might be influenced by variables we don't think of, but to avoid letting ongoing arcs (like the Greyjoys' go totally off-screen for too long stretches is no doubt a factor in play for the show runners.
It sounds quite possible this is the point where they will start to more significantly re arrange the material and depart from each novel's structure as they see fit, perhaps tweaks the timelines/sequence of events when necessary. Books 1-2 were easier to more or less follow and arrange into the 10 episode format, from here on it's less obvious.
It seems your guess is right and they've worked the Greyjoys into this season somehow - how exactly and to what extent is anyone's guess. I don't follow much the GoT news, but I've seen Alfie Allen (Theon) was with the rest of the cast in some of the season 3 media events.
That they'll work Joffrey's wedding, Tyrion's arrest and Sansa's escape in the season 3 finale is a good guess.