I have not disconnected the BCM. Last time this happened I had simply switched the IMA switch off and the car was able to run. I ran it two weeks or so this way previously before I was able to swap a new pack in. I can certainly disconnect the BCM connector easily enough if it really needs to be removed. With all the work I did on my pack over the past several months trying to prolong it through deep discharge/recharge cycles to no avail, I did not bother putting all the screws back into the battery compartment cover. Figured I would be going in and out a lot.Did you also unplug the BCM? This should allow it to charge the 12V properly until you can figure out what you want to do.
Talk to Eli at Bumblebee for your battery needs...
I found an older article on this site at Which is BCM and MCM? which shows removing the endplate from the battery stick assembly leaving only the endplate and MCM installed. I assume this is a similar idea without bothering to disassemble the pack.