Where are you getting the idea that a lot of admirals are also members of the Federation Council? I haven't seen any recent'ish novels or anything in canon indicate that, but maybe I missed something?
There's also the episode Rapture
, where Bajor's admittance to the Federation is presided over by a Starfleet admiral, not someone from the civilian government of the U.F.P. Not to mention that the scene where the ceremony is to officially take place (until Sisko ends it with his visionary warning), where almost 75% of the people representing the Federation are from Starfleet.
As for Shakaar
, here's my problem with it - it's shallow. Neither Shakaar nor Winn is allowed to argue their case convincingly - it's all too rushed, as TheGodBen
points out, and all this important information is jettisoned. Now given that I'm a libertarian, I'm inclined to take Shakaar's side, most especially when the shock troops are sent in. But he just comes off as too stubborn. If they had taken the time to outline why the situation in the province was so bad, it would have helped. "Feeding our people" just isn't enough of a justification. Are we dealing with a famine? Are we dealing with massive numbers of children suffering from malnutrition? You got to give me something more concrete to argue against Winn's desire to spur the entire Bajoran economy.
Then, of course, there's the problem of Duncan Regehr having absolutely zero chemistry with Nana Visitor. And I have a hard time believing this guy had the force of personality to hold together a struggling resistance cell, just saying.
Overall though, I do think it's an above average episode - maybe three stars, as it's definitely libertarian in theme. We have a government that fails to keep its promises, a local leader facing a hopeless situation who is sick of said government and an villain who is willing to bring about the "collective good" at the point of a gun. Good stuff. It's a shame it's harmed by a mediocre script and acting.