I think there could be problems. Firstly, if the second battery is low you may exceed the current rating of the fet, it is not a defined load like a resistor.
Also when the second battery is fully charged there may not be enough drop in voltage to reset the comparitor. If I have got it right this means no pulse to turn on the 555. I think the 555 is connected as a monostable and if so there will be no signal to fire the gate of the fet and it will stay turned off until the wind drops and the comparitor regains control.
If you want to charge this second battery I think you would be better off with a controller using a relay and with hysteresis across the comparitor (Hugh's circuit would do if you have the book). You could use this as a first stage diversion and when this battery is fully charged your main diversion control would come in as normal.
Flux