So I've actually done this before on large li-ion battery packs, just not on Zero. Your thought process is correct. The BMS will refuse to charge the battery pack if the voltage on one or more cells is too low. Since I haven't opened a Zero battery pack before I can't tell you what you need to remove or what wires you need to connect to, but you're correct in what you need to do. You'll need to open the battery pack, find the common ground for all cells and connect a charger ground to that. Then find the positive wire for each cell and one at a time charge them up to a more acceptable voltage. Alternatively you can find the main battery relay and bypass it, basically forcing the battery to be enabled, and then see if the on-board charger will charge it.
Now for the (hopefully) obvious, you need to be careful doing this. A typical car 12v battery can do some serious damage if you drop a wrench somewhere, this battery is magnitudes more powerful than a car battery. You need to wear rubber gloves, you need to do this in an open area away from flammables, you need electrician tools not standard bare metal wrenches/screwdrivers. Basically act like you're doing surgery to a sleeping alligator, every move must be slow and precise.