^^ First off, Hillary never said "consequences" for Pakistan. She was pushed to clarify and she refused to. I explain this in one of two ways; she is a politician at the end of the day, rather than a career diplomat, so she could have said something realizing she shouldn't have said it and then refused to go any further with it leaving the ambiguity which she could use as space to backtrack. It's either this, or she meant consequences for terrorists and this has been misconstrued, as Holbrooke has now publicly clarified.
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It can't be the bold option since she said that if the attacks are traced back to Pakistan there will be serious consequences. It cant be that there will be consequences for Terrorists only if the attack is traced to Paksitan and not other wise??
I think your 1st possibility makes more sense...
Or may be as Deepak says, its a good cop bad cop going on...