All that you need is to monitor the output voltage and then drop out a power contactor when the minimum voltage is reached. Normally, that will be between 1.9 volts per cell and 1.75 VPC. Alternative power systems normally use the 1.75 VPC @ 25°c as the cutoff point.
I have a 48 volt stack running a telephone system and since we keep them at normal room temperature, we only need to monitor the voltage. We are using Absolyte batteries so you can beat the crap out of them and they still have a 20 year life expectancy.