Also he presents the Clarke line describing Rice as "disengaged" as if it had a factual basis...
I'm not sure that this is what Novak is trying to say. I think he means that Clarke & Rice didn't have the same working relationship that Clarke had w/ Sandy Berger. The sentence is somewhat ambiguous--my first take was the same as yours.
Also the memos where Rice requested Clarke start attending meetings he was missing go to it being a two-way street and not a matter of a disengaged Rice not holding meetings or not wanting to deal with an issue she was in fact very much dealing with.
So I do think by leaving out those aspects, Novak's analysis is flawed in that area.