I took the implication to be that the post-worm hole Jor El had been on a rampage of sorts to get Jon back leading to his being a criminal. He was operating openly and without any issue prior to that point. The crystal queen was actually the one using Rogal Zaar and was behind the destruction of Krypton. She was killed in Supergirl. The Guardian that was part of it was already dead as well. Zor El was dead. Starfire's father's dead as well. I think that's pretty much it for the Circle.

I've said this several times, but Bendis' run has been a lot of good first draft stories that one or two passes to tighten the ploting up and tweaking the characters actions just a little would make if fit and flow so much better. Lois' story in particular could have worked out so much better.