Brake rotors are subject to a number of different forces that can cause them to corrode or to collect damaging deposits. Wire-brushing is a viable way to clean a rotor, provided that you follow a few simple rules.
While some hardened steel rotors might be able to withstand the intense abrasion of a steel-bristle brush wheel, most cannot. For power tool applications, use only a brass wire brush on the rotor face to eliminate flash rust and deposits. Steel bristles are safe if you use a handheld, toothbrush-style brush.
Apply light pressure with your wire-brush wheel and move in quick but steady circles while holding the grinder at roughly a 45-degree angle to the rotor face. This is as much to keep brass wires from flying off of the wheel as to protect the rotor. These wires can easily embed in exposed flesh when they fly off of the wheel.
You should only use a wire brush to clean light to medium rust or deposits off of the rotor surface. If the rust has penetrated the rotor face enough to cause visible pitting, you need to replace the structurally compromised component before it shatters under heavy usage.