No bad guys are good guys. And most good guys are not good guys, either.
The Shadows, the Centauri and the PSI Corps are introduced as “bad guys” but gain a lot of positive aspects during the show without becoming “good guys”. The Nightwatch and the Earth Governement under president Clark are “bad guys” – but quite a few of there supporters/members become important “good” characters, like Zach Allan, Elizabeth Lochley or Susanna Luchenko.
That’s my point about the Babylon 5 series – they deconstruct the good guy/bad guy meme. Mostly.