I don't believe that a different pad choice would make the rotor any hotter. Its been a long time since I took physics but to stop the bike you have to dissapate stored energy (Mass x speed) by using friction. This changes stored energy to heat which is stored in the rotor. The pads themselves store very little heat, so most of it soaks into the rotor. If the mass remains constant, and the speed is pretty much the same (let's say you are braking from 40 mph to zero on an average) your rotor won't be any hotter if you use a different type of pad. Possibly the new pad may do a better job of producing friction, so you rotor will heat up quicker... but it won't do it as long as you will stop quicker.
Rotors get very hot as you use the brakes. I'll bet WilburT can tell us stories about smokin' hot lugnuts on cars, I've had them come off so hot they will burn you. The heat from the rotors will soak into everything, the hub, the wheel, and so on. Its just normal. You can cook a rotor with high speed panic stops, or having the caliper partially enguaged for a long period of time because you have your foot resting on the brake pedal.