Industrial isopropyl is absolutely fine for rotors and pads. I've used the 70% stuff and 99% stuff in the past with good results. Don't forget to clean the inside edges of the cut-outs in the rotor as dirt/contaminants can stay trapped in those pockets.
For contaminated pads, I've found that just using alcohol is not enough to get rid of brake squeal if it's deeply contaminated. Use sandpaper, then wipe away with alcohol, repeat if necessary. Boil the pads or blowtorch 'em as a last resort. Contaminated disc pads are trickier to 'save' than rotors, usually. Sometimes even all these steps are not enough to save disc pads from howling, in which case it's new pads time.