Yes I agree, it seems dumb doesn't it? However this shutdown would never occur if the firmware reads the voltage correctly, as I presume it does in 1.6.
I think the battery protection scheme is to prevent ruining the battery in the case where you accidentally store the bird in the case without turning off the battery. I've actually done that, but discovered it when I got home and removed the sd card. Dumb mistake but I can see it absent mindedly happening under several circumstances. Taking battery cells below 3.0 volts will do damage, hence the protection.
Then I think, why didn't they put in a simple requirement mandating the craft must be grounded to start battery protection?. Maybe they did in the 1.6 battery firmware..... I'm not sure. I'm hoping they did, given the catastrophic consequences of shutting down power mid flight.
