There's a setting in Thunderbird that lets SAV (or other AV) grab only the infected message rather than the whole Inbox file.

Tools->Options->Security->Anti-Virus tab:

Check "Allow antivirus clients to quarantine individual incoming messages".

I'm still getting trojan attempts, and SAV still takes forever when it finds one, but at least it's not grabbing the whole Inbox now.

Cheers,
Scott.