the groove in the rotor is normal, however it's not *supposed* to be rusty. probably a failed gasket let moisture in while it sat. I'd just clean it up with a wire brush and some rust remover (the brand is escaping me) and make sure it's lightly oiled to keep from re-rusting.
As far as the primer goes, the "rust-colored" primer is OK, however most primers will cover the rust with whatever color they are, and ideally you're priming with an appropriate color to the final paint. did i read that you're going with blue? might want to try a grey primer to affect the color less, although if it's good opaque paint it won't be an issue either way.
my suggestion is to use rust reformer primer 1st if that's not what you have. it chemically converts the rust to an inert compound which prevents it from catalyzing more rust -- rust creates rust. if you just paint over rust, the rust will still grow.