Several people have converted their strat to a single pickup setup, both just bridge or just neck (including myself on occasion - and I like the idea myself of just middle as I rarely use bridge or neck pickups), but I am not sure I see the point in your case.. If you are going to just leave the other pickups there as 'dummies', just leave the switch in neck position and everything functions as you want without modifying the wiring or functionality.
If you want to make a real point of it, just rout out a blank scratch plate without the other pickup holes and a single volume and tone so it looks like a single pickup version (neck in your case). If you have the other pickups in place no one would know the difference.