The Libby case is different because what Bush did was commute the sentence for someone who was committing a bad act on behalf of Bush (and Cheney).
It isn't that the President exercised his constitutional powers, it is that he is furthering a cover-up. That is the sand in the eyes of Fitz's umpire.
The outrage is over Bush's continuation of the cover-up. Had he not commuted Libby's sentence, then the DOJ may have been able to extract information from Libby as to why he lied in exchange for a lighter prison term.
So, in spite of all of his protestations over the years that he wouldn't comment on the Libby case because it was in the justice system, Bush's action just pulled the rug out from under the Justice System.
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