Is it detrimental to an SMPS to turn it on and off frequently?
EDIT: Oh damn! I see you have NFETs as low side switches already... I guess my post is not so useful to you. As tcrosley mentions the whole operation of the converter is "ON/OFF" constantly anyway, so if you force it off for longer it will be okay.

MY SUGGESTION WAS:

I highly suggest you just use a spare digital IO line for each, and some P Channel MOSFETs as high side load switches. Let the Switching converter idle with no load, maybe keeping a nice fat 1000-2000uF capacitor charged nearby, before the P FETs. Then when it comes time to turn on the rudder/winch servos, in firmware you should first turn on the high side P FETs and wait 100ms for the power supply to settle just in case, and then continue with your signals/movement. 

I have made a fancy schematic diagram for you to explain what I mean.