Regarding loss of civil liberties:
In an ideal world I would be free from both disorganized crime and organized crime (including state actors as organized criminals).
If that's not available to me, I would prefer to be free of more serious crimes (regardless of who commits them) and to enjoy a greater degree of liberty (regardless of how it is enforced).
So I would prefer to lose free speech than to lose my right of self-defense against burglars, although ideally all of my rights should be fully intact against all comers.
Regarding rule by the military / raw power:
I think raw power is always what rules in the short run and the power of ideas is always what rules in the long run. I don't see how rule by the military is any worse than rule by the psuedo-military we call police. Moreover, being open about the nature of power allows the citizenry to react intelligently, in a way that most struggle to do when power is masked as "the people" ruling "themselves".