Yeah, I seriously doubt the Smith/Moffat falling out story. From everything I've ever seen, Smith seems to absolutely adore Steven Moffat, and considers every script he writes the most "brilliant" thing ever.
And I just don't see Moffat being that petty about the Eccleston situation either. He probably knew from the start
that Ecceston's involvement would be a long shot, so why get all petulant about it when he finally said "no"?