I'm relatively certain you can make MC do this by editing the ini file. Again, make backups and do this at your own risk.
Another way to do it, might be easier: Say you have library O and library G. (That's the (O)ld library and the (G)ood library)
You want to get rid of O and keep G, but MC won't let you delete O. So just transfer G over to O.
Back up G. Remember where you put the backup file. Switch libraries over to O. Now restore into O from the G backup. Now O and G are the same. CONFIRM THIS. Now all you have to do is delete G and then rename O to G. That should do it.
Brian.