Halfway through correcting it now. Chipped it out with a screwdriver, cleaned it with a Dremel wire wheel and rust converter (mostly phosphoric acid gel stuff from Rustoleum), and sealed it with primer. Next up is Bondo filler putty, sand, then reprime and paint.

One comment, Nissan HSLA steel is pretty magic, there was water inside the rust bubble when I chipped it out but plenty of good metal left underneath. It was nowhere near working its way into the roof liner, which is what I was worried about.
When I'm done, I'll take photos that explain how to get the roof rack off. It's a lot easier than you think. It The rail pivots on the center mount to an angle...slide back, then it pops right off.