I think Bob really enjoyed the acting he got to do in season three--he seems to enjoy portraying those dark, morally debatable storylines and has mentioned that he liked the challenge of it. But yes, like us, he was frustrated with the stuff that happened "off screen," which ultimately amounts to a pacing problem.
I am still not one of those fans who thought it was uncharacteristic of Bellamy, though. Negative development doesn't make it out of character.
Season three Bellamy does set the stage for season four Bellamy, though, and season four Bellamy is my fave, so . . . "From the ashes we will rise" really ended up describing Bellamy in season four, in a way.