Well, a couple of things.
First, you can interupt the power wires of the GPS cable, to turn off the unit. You can do this manually, or you can use some sort of relay controlled by a computer controller.
The other thing is, GPS units are RECEIVERS, and do NOT transmit. While it is true there is an oscilator in the unit, and that can cause some very low level RF, it shouldn't cause any interference to other communications devices. What frequency do you think is being affected. The EASIER solution is to seperate the antennas by at least a wavelength. Since GPS is in the 2.4 gig range, you can get significant isolation with just 5 inches of seperation, though the more, the better.