Yeah, we're told that the Empire has been bad; I actually think the show should be showing it. The Ferrix thing, after all, is a police action that goes south quite badly; it's the result of poor planning/incompetence rather than because the people behind it are actively trying to be evil
I think the problem the show has is, weirdly, something early #BlakesSeven got right (until the third series onwards): in seasons 2 of Blakes 7 the Federation is complicated and nuanced; it does bad things in order to maintain general control for the benefit of the masses.
This is why Blake looks increasingly unhinged as the series 2 goes on, because his rebellion seems to be about bringing down the system with no idea of how they would maintain order afterwards (leading to Avon's best moments).