Due to a flaw in my schematic, I needed to rearrange the electronics and split the control system in two entities. Here's a simplified schematic showing the power management. Not drawn here is the 5V regulators for each of the two MCUs.
The sole purpose of the "Battery MCU" is to measure the voltage of the battery and disconnect it from the rest of the system when the voltage drops below 3.0V/cell. I might also use the MOSFET at the bottom as a shunt to calculate the voltage sag and compensate for that.