Percentage-wise, the GPIB power is probably no big deal. I don't know how the GPIB option is connected internally, but if it's say, via a ribbon cable, you may be able to just unplug it and secure it so it can't short to anything. Then make sure the system starts up and runs properly without it - it may cause error reports on POST, for instance, if it expects to find it.
If the GPIB module is hard-plugged directly into a port, and requires physical removal to disconnect, then you'll have to worry about plugging the empty cabinet hole, and the possibility of eventually losing the GPIB parts - this tends to happen when things are separated.
The simplest thing is to just leave it be.
Ed
