Too bad about the finish being wrecked!
I noticed that Sonax wheel cleaner was starting to get hard on my brakes as well so I am no longer going to use it, P21S is the best wheel cleaner there is when it comes to being gentle on brakes.
As for your questions on repainting, I would look into having the hats re-anodized since paint may be susceptible to damage/peeling due to wheel changes. Painting the yellow by hand is an option or you could use an x-acto knife and mask it up...... your choice.
If you can be without the car for a while I strongly recommend contacting IND, they paint lots of brakes and can do them in any color you want. If you explain that you need a quick turnaround I am sure they can expedite the process too!
2011 E90 M3 ZCP - Individual Moonstone/Individual Amarone Extended/Individual Piano Black With Inlay:LINK!!!
1994 Euro E36 M3 Sedan - Daytona Violet/Mulberry:LINK!!!