So - some proposals in this thread are to destroy S31 and create a branch of starfleet intelligence that uses the same amoral methods in pursuit of the same goals.
Same difference.
Just bring S31 into the fold - to become answerable to the democratically elected leaders of the federation (and, for all we know, it already is - that's definitely NOT something Sloan/S31 would advertise) - and you have your highly efficient espionage/black ops agency, as opposed to a bunch of rookies that don't know what they're doing.
Mr. Laser Beam wrote:

Not even the blackest of black ops organizations would stoop that low.
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Eh...to be young and naive...