I've run into the same issue.
Depending on what AV version you are on, at one point in time you could script the removal of the file extension in the Quarantine folder .qar I believe
(there's a few other posts on this topic).
I am on LANDesk AV in 9.5 (rebranded kaspersky 10) and tried scripting to remove the .bak from the QB folder but the files in the local console would not get removed, even after a forced vulscan.
I have shelved the idea lately, I hope someone else has luck with this, I'm in the same boat.