I pretty sure she was eventually forced to leave by Strauss who pretty much said she had to go to the new job or they would make her and they did. Guess she has more power than most. At the end J.J said this quote which sums up her feelings and the reason for her departure.
JJ: I'm thankful for my years spent with this family, for everything we shared, every chance we had to grow. I'll take the best of them with me and lead by their example wherever I go. A friend told me to be honest with you, so here it goes. This isn't what I want, but I'll take the high road. Maybe it's because I look at everything as a lesson, or because I don't want to walk around angry, or maybe it's because I finally understand. There are things we don't want to happen, but have to accept. Things we don't want to know, but have to learn. And people we can't live without, but have to let go
T.V.com for the quote.