In the light of the last events, I think i'll go for the classic version instead. Is there any way I can 'downgrade' to 3.1.4 apart from a fresh install?
I wouldn't bother, the fact that 3.2 is in RC status mean's that 3.2 is about to be released. It should be released very shortly.
I notice you have a .svn folder in there, how did you install the 3.2 RC? by using SSH on the Dreamhost cli, or by downloading the .zip and uploading the files?
Is this something you can reproduce? (Ie. try to update again, after backing up your files, does it remove the themes folder again?)
If this is a bug, this is the first report of it, and there's been thousands of RC installs, it's something we need to get on top of :)