I think it clicked after a fashion, but Johns definitely took time to figure her out. Had he stayed on following the resolution of her arc, I think we would have gotten a more traditional Karen. Compare her at the start when she joined the team and she was more like we remember the character.
He was tasked with restoring her history and there's no way to properly do that without really putting Karen through the ringer. You can't really have her discover her friends, family, planets and universe are dead and that she's been replaced with her just sassing over it. That's a bridge too far, y'know?
Using Karen as the conduit to connect our universe to a dead one is going to lead to her not being in the best spirits. I can understand objecting to that decision, but the execution is sound.