I really don't see that being the outcome. The Skype stuff will probably just be in parallel to the XMPP stuff. In fact, I wouldn't put it past Skype to try and get Facebook to shut down the XMPP stuff so more users have to use Skype clients to even text chat outside of the Facebook website. Big companies like walled gardens and proprietary protocols.
What I'd have much preferred to have seen would be a XMPP-video based feature, a-la Google's GMail/XMPP Jingle video. Incidentally, does anyone have any idea why the GTalk client doesn't support it, but ruddy GMail and the N900 does? ...the mind boggles.
The lack of any decent Jingle clients on Windows isn't such a hurdle if Facebook were to use a browser plugin like GMail (or indeed, sort out using the same one).