5 pages of threads and not one about the blatent use of Karl in the episode.

It seems like the producers wanted us to see Karl working with the others. They could have just skipped past him and had Juliet just knocking on Ben's door.
He must have been quite significant as he developed the x-rays for Juliet.

Any thoughts on why Karl was in the cages and brainwashing room.

My guess is that he was working with the others until Ben found out about his relationship with Alex. Now here's the far fetched part but maybe Karl knows something about Rousseau. This could be why Ben doesn't want him with Alex because he might tell her the truth about her mother.
(Although Karl in the cages could just have been a plant to show Sawyer the capabilities of the others)

Any thoughts?

Well if getting pregnant is a death sentence

Yh true.

I didn't think of that one

Nice one