Comment 5 for bug 871068

If you feel like opening a text editor and know a bit of XML, you can add a line into ~/.config/banshee-1/addin-db-001/config.xml, which is where the state of extensions is stored.

The file looks something like this:
<Configuration>
  <AddinStatus>
    <Addin id="Banshee.UbuntuOneMusicStore,1.0" enabled="False" />
  </AddinStatus>
</Configuration>