First, let me say I do like the idea of a companion being kidnapped. The problem is choosin which one. It would work better as future companion stories in my opinion.
I think if you done a hostage type story that the players would get a main companion taken away and the storyline would be that of a resuce and save to get her or him back. You could some how work Jaxo back into the story.
Bringing back Ava Jaxo I also support. I wish we could have gotten her as a trooper companion. The only problem is that the only way she would return is if you saved her. Her return would be based on the indiviual players choices.