I agree that the Black Widow thing wasn't well-handled. In the issue, she had doubts about letting him continue on with her, so dropping him off made sense. Sticking him in a prison made less sense particularly because I find it hard to believe she can just insert him into prison, unless this prison is just completely without due process. And I wouldn't understand her motivation for wanted him imprisoned anyway. Why not just drop him off? What harm was he doing?
I really feel like we could've skipped the previous arc and just gone straight here.