Not entirely sure what your asking but thought I would comment:

The MCLR pin on some PIC devices have a max voltage of 9 volts, 16F1527 for instance, but some device programmers can generate voltages as high as 13.5Volts on this pin. This means you should add a series resistor and clamping zener diode on the MCLR pin for such devices.

As far as configuring the ICSP pins in your code, I've always just configured them as inputs, and relied on the hardware programming algorythm built into each device to handle all the details during the programming cycle.

Get's more complicated if you use the ICSP pins for functions other than dedicated programming pins.