I've done countless pad changes without touching the rotors, and never had a problem. Heck, on my old Honda I wore the pads down to bare metal, and it ate into the rotor, leaving a big gouge in the rotor. I slapped some new pads on it because I couldnt afford rotors at the time, and went to inspect them a week later and the rotor was like new again.

If it makes you feel better, hit the rotor with some sand paper.

88 4R, 350 V8, R150 5 speed Sold <...uot; />
97 4R, stock, daily driver
98 Sienna, kid and dog hauler, wife's ride