I updated to SourceTree 2.0 last week. This morning, got the 'update available' message. Updated. It unistalled 2.0 and reinstalled 1.9. Immediately upon completion, got '1.9 is not supported' message.
I've filed a support request. Will update when I get a response.
Edit: I've noticed that 2.0 is installed in users\username\AppData\Local. I unistalled all versions of SourceTree using Control Panel -> Programs and then reinstalled 2.0.
I think the takeaway here is that you should manually uninstall all older versions of SourceTree before installing 2.0.