Rust on the pole pieces, at least if it's only a bit, will not affect the sound of your bass. I agree that it can look bad, but unless moisture gets inside the pickup itself, it's not a big problem.
You want to be extremely careful if you decide to try to get the rust off the pole pieces. If you use something metallic or sand off a small bit of the magnets themselves, you'll never get all the metal filings out of the pickup and that WILL cause real damage.
I'd either leave it alone - if it's not affecting the tone of the bass - or, if you have noticed a difference, then replace the pickup.
good luck!
Jack