another possibility:
Blair is on his way out, Brown probably on his way in.
Blunkett wants a job.
Blunkett publishes a book saying Brown was against the war. This encourages Labour voters who also oppose the war to think Brown is a Good Thing.
As a result of this, Brown gets the top job.
Blunkett gets back into cabinet.
I may be too cynical here, but it is worth considering the timing of Blunkett's book.
As for Brown being under Blair's thumb - well, that's his job. Any prime minister is the leader of his country and while other ministers may oppose him in private, they must weigh the consequences of making their disagreement public, as jake says.