Putting her in State is either asking for trouble or revealing that he's not in as much disagreement with her as previously thought.
There's a third option: Obama is putting people in positions that mirrors their experience. Just because Hilary starkly contrasts Obama's foreign policy doesn't mean that Obama is going to be bowing to her. As the Sec of State she can flex her muscles, push the Obama policy, and we, as Americans, can know that she won't be bulldozed by hawk governments. If in a year we see comments from her where she is trying to run her own show, then we'll hopefully see Obama correct his mistake, but Hilary hasn't indicated that she wants to use the position to further her foreign policy.
If Obama made a dove Sec of State, plenty of military minded Americans would be crying out how America is setting itself up as a weak state to be fucked with.
Remember, these people still answer to Obama, and he has shown that he commands the respect of others, so this won't be as divisive a cabinet as Bush.