The detail here is that, in theory, humanity has progressed so much into the right direction that we really shouldn't need something like S31, that's why it's shocking for all of us. We deal with a few random evil admirals, but we know they eventually received their rightful punishment. Starfleet is not just top competence, it's also top ethical and moral competence, or it should be. Maybe it was needed for the first years of Starfleet, but now it should be just a leftover of what they were. They could be only "called" during wartime or some special emergency (say, Borg invasion).
Think about all the times Picard and his crew have faced serious ethical questionings and they still didn't need S31 to do the job for them.