Absolutely don't touch the rotor unless it is warped or otherwise giving you a pulsating feel as you brake. Nothing can be gained and you just loose that much wear potential. I ran the pads down to the metal and gouged my rotors up pretty bad when the truck was new. They wore out in less than 20K miles. By the time I got home they were pretty bad. What to do, --- find a shop that could turn them on the truck or go through the expense of removing the hubs. My rotors are not removable like yours. I decided to put some new pads on and drive around while I hunted for someone who could do the work. I just kept driving and my brakes have great feel. By the time those pads wore out my rotors were smooth but groovy. The truck has 235K miles on it now and my pads last 40 or 50 K miles and the brakes are silky smooth. As I came to this experience, I did the same thing to a couple of cars the kids did their thing to, and they have turned out the same way. If no pulsating leave them alone and enjoy the wear.
I expected that there would be a pulling to the left or right with one rotor groovy and the other flat but if that occurred it dissappered within just a few miles of driving. I expect that the way this all turns out would depend on the kind of material in the pads. I forget at the moment the kind of pad but I keep the old box behind the seat and buy the same thing again each time. They are much better than what came on the truck both for braking power, feel and wear. Your milage may vary but for sure the pads will smoth out the rough rotor.