I've read whole thread and have few ideas. First checking voltage to check if battery is drained it's great but to check what's the status during charge cycle requires to disconnect battery from the power source. But there's slightly different thing that can be done. You can measure the charging current and if it will drop below specified value you can turn off your alternator.
And another thought just to turn on alternator during engine breaking, it can be done easily with a preasure switch since during engine breaking mainfold pressure hits the lovest values. Isn't it?
I think even if the FE % gain is small it's worth to think of because every bit counts.
For sure I won't delete alternator in my Previa, because this car is used mostly for longer trips. And to carry deep cycle baterries that will last for 1000+ kilometers will kill my FE anyway
But again if we could automate the process of charging battery I think I would go for it. I'll try to find out if my alternator can be easily switched off and I'll try to figure it out how to automate this process in my car.