First, thanks to Milcommoguy for the heads-up on this. I just got my first A2 vehicle, and was just about to throw in a simple disconnect-ground-switch. That´s definitely not enough. I was glad I found this here just in time.
However, I´ve been thinking long and hard about this, and I wondered why the TMs don´t mention the problem of the 12V take-off. Cutting off ground with a switch is the same as taking off the ground cable from the second battery during maintenance.
I was also worried that two relays, even when activated at the same time, might create a voltage spike in the electronics due to slightly different mechanical timings for opening.
So I took an amperemeter, and checked for the actual current in the 12 V output while everything is off. The lead is numbered "290/291/537" by the way, and in a stock M1045A2 (I don´t have any other 12 V gadgets in yet), it´s just running to the TCM, and to the tranny relay (which is off when "Run" is off). There IS in fact a small current flowing to the TCM, even in a completely switched-off Humvee, of about 3.0 milliamps.
This means that by ohm´s law (at least at rest), a TCM has a resistance of about 4 Kohms, which is quite a lot.
I´m convinced now that, yes, a second relay in the 12 V take-off makes sense (at the very least to stop that 3 milliamps from slowly draining your battery). But I think that due to the quite high resistance of the TCM there is no immediate danger when you take off just the ground cable on the second battery.
But I´m just a mechanical guy trying to understand electrics, so feel free to correct me.