For your own vehicle, if the pads are not worn much, as you describe, just scuff the friction surface of the pads on some 60-100 grit which is laying on a flat surface. This will allow the slightly used pads to break in with the new rotor surface together. Done it several times, no problem. Some of these newer vehicles tend to warp the rotors well before time to discard the pads, which are perfectly usable yet. Found it to occur often on 2002-2003 Expeditions. Or you can just throw away perfectly good pads and buy some more...
If the old rotors can be resurfaced and still used, why not go that route? Here I can get machined for $7 each and some places are $10 each. Unless you have the kind that cannot be resurfaced.