First, from a real-world perspective there is the issue of television as short-story instead of a novel, i.e. we do just get a few snapshots and not the entire picture so we often (I only remember that Pressman faced court martial) do now know what happened after an Admiral violated the law.
Second, there is the not-so-nice point I made some time ago about Section 31 being the dark underside of the Federation. Like in the real world many people are basically fine with some nasty sh*t being done by the military as long as the fascade which helps you to pretend that everything is fine and dandy is intact. In short, the UFP is hypocritical.
While especially DS9 with Red Squad, Leighton, Ross and S31 hinted at this TNG already made some suggestions along these lines; e.g. when Pressman was arrested by Picard he said that he has "a lot of friends at Starfleet Command". Of course he could just be lying in order to deter Picard but he did after all not act alone.
So I think that the supposed utopian Trek has often portrayed the frequently occuring abuse of power of the military in a fairly realistic fashion.
About Nechayev, I think she qualifies (unlike Marcus) as hawk proper but not as criminal. Sending Picard on a secret ops mission into Cardassian space or wanting to use Hugh as a weapon are debatable decisions but in my opinion they are definitely not criminal or clearly wrong.