Thanks for the suggestion. I was starting to think along these lines, but I'm much clearer on the actual problem now thanks to the feedback I've received. Looks like there might be some solutions from the RC community who are using LIPO packs that are damaged by under voltage, so I'll check these out next. Was hoping to get something off the shelf, but haven't found anything so far.
I think system shutdown is the most desirable behaviour. Part of the problem is I don't know how bad the voltage drop is as, since the robot is mobile, it is difficult to measure. I've found some LED voltmeters that I should be able to mount onboard for testing, so this should give me some insight.