After 3 hours isolating this to the minimal expression (which is tedious if your add-in is has lots of user interface items and debugging a VS 2010 add-in on a virtual machine is painfully slow), here it is:

VS 2010 Beta 2 Bug: deleting a CommandbarPopup unloading add-in causes VS to disappear
https://connect.microsoft.com/VisualStudio/feedback/ViewFeedback.aspx?FeedbackID=503093

(the problem happens if the add-in creates two (not just one) CommandBarPopups on a parent CommandBarPopup and tries to delete them when unloaded)