That's called bedding in the pads. When you have a fresh surface to work with (i.e. a new or resurfaced rotor) you want to build up a layer of pad material on the rotor to make sure everything works alright. That won't really affect the rotors other than put them through a few heat cycles. It won't hurt, but bedding in your pads isn't some rotor fail-safe.

The best way to keep your rotors from warping is to keep the lug nuts torqued to spec. If you want to get some added durability you can have the rotors cryo-treated.