So, I thought I'd follow upon this.
The procedure is really quite easy, raise car, support on jack stands. Remove hub cap, lug nuts (19mm), wheel/tire, remove caliper mounting hardware (17mm) x2, remove caliper and support with wire hanger. Once the caliper is off the rotor isn't held in by anything and can be removed to be replaced/machined. To compress the caliper piston (one on each caliper) grab a 4" or 6" c-clamp, loosen the bleed screw (5/16 box end wrench), tighten clamp until piston is compressed and re-tighten bleed screw (just snug tight). Check brake fluid level, top off if necessary. Replacing the brake pads are a little tricky, remove old pads and pay attention to how the springs hold the pads apart, and how the two clips pinch the pads in place. Place the copper clips at either end of the caliper, install new pads (one at a time, and it can take a little persuasion). Once the pads are in place and seated you can install the springs; this is most easily done if you squeeze the spring together and insert them through the rear of the caliper. Now the new/machined rotor can be installed in the hub (it just sits there). The caliper can now be installed and secured with mounting hardware (found in a Mazda forum torque bolts to 29-36 ft/lbs). Install wheel/tire, lug nuts and hub cap. Before driving start the car, let idle, actuate the brake pedal several times to regain pressure; go for a test drive.
So if anyone has to do this for an '01 protege, there's my write up. Hope it helps!