Two questions:
1) Aluminum or steel frame?
2) What's the original finish? If it's not blued then the blue won't match exactly (and, bluing is not a great rust preventer anyway). If you want to go super-cheap even permanent marker can work just to cover.
Personally I'd gently flatten out the high spots and just shoot it. The spots on my handguns that rust are the ones that get handled a lot, particularly the rear slide and sight area.
Its a Sig and their site says it is an Alloy frame. Original finish. I'm not so worried about it matching just rusting. That spot is right where my finger goes so it's going to get a bit of sweat and whatnot. Hopefully the blue will hold but sounds like you don't think it will.