Who knows how much of her BPD is related to the failing relationship or the drinking. 17 years is a long time to be with someone when neither of you knew of the illness. What has the 17 years been like, looking back with the added knowledge that she is bi-polar? Certainly being an alcoholic doesn't help matters. I'm alarmed at the clonopan and drinking though. Clonopan doesn't sound like the right anti-anxiety drug for a bi-polar anyway, I know many who became more aggressive with clonopan.
I think the only thing you can do is try to recognize that being diagnosed only 2 weeks ago could be having a negative effect on your wife, and she is acting out more because of it. She may also be acting out in ways you are not aware of...yet.
If she is unhappy with her life then maybe some talk therapy might be in order. If on the other hand, she's unhappy and has been unhappy in the marriage, then you need to let things play out. Let her leave if that is what she wants, otherwise she'll resent you for trying to keep her somewhere where she is unhappy.
If you haven't already, read up on BPD, might come in handy.