Disclaimer: I'm a Tor newbie and networking stuff isn't my strong suit, you probably know more about it than I do.
But: I fixed a Tor-related bug for version 0.6 a few days ago. In particular, I moved all of the "turn this on or turn this off if running over Tor" to one spot (in the init.cpp file) and reworked the code so that you can override all of those decisions via command-line or bitcoin.conf switches (e.g. specify -nolisten=0 to set nolisten to false so you DO listen even if running a port 9050 proxy).