Your pulling the pads anyway, cover the disc the best you can (get some brake cleaner to clean it again BEFORE re-assembly) and spray where ever you can get to the theads.
I sprayed both ends of the bolt. I just took a piece of cardboard and made a "shield" for over-spray on the discs while spraying. It's kind of awkward getting to the thread end of the bolts as you have to spray from the other side towards the caliper, but turning the forks makes thing a little easier to access. I immediately rinsed off what I could when I got over spray on the brake components with brake cleaner, and soap/watered any painted surfaces (since I'm still not sure how PB interacts with paint, although it did make my tire nice and shiny in the one spot it dripped there).
Then just clean the crap out of everything before you put it back together.