So what do you imagine Section 31 is like in the MU? Are they like their Federation counterparts, taking out the Empire's enemies from the dark? Or are they less secretive about their existence, sort of like a state police (or Gestapo, if you don't mind me drawing comparisons)?
Gestapo is a good way to think about it. You already have the fear of assination from lower ranks, now you have a state police that would hessitate to blow you whole crew out of the universe if you didn't do the Empires bidding.
These two are just commissions, but that is the idea I had a few years back.