Re: upgrading to BP1.0.2
The only plugins that need to be deactivated are those that are dependent upon BuddyPress. So, if you don’t have any of those in mu-plugins, you should be fine keeping them as is.
Andy is working on some code that will automatically deactivate all BP-dependent plugins whenever BP gets deactivated. Of course, this code will need to be retroactively added to all current BP plugins out there, but I imagine plugin devs will simply add this coding to one of their next versions.