If you want to take the time, I would edit the sourcecode for the sourcebans plugin(s) and change it so it reads another file instead (i.e. sourcebans1.cfg and sourcebans2.cfg) for each server. Have the server load the plugin independently from each installation.
Assuming you are using 1.5.2F you would need to edit:
- sourcebans.sp (Line 307)
- sbchecker.sp (Lines 2452 & 2457)
- sourcecomms.sp (Lines 2571 & 2591)