I would strip the seasoning completely, deal with the rust and then re-season. To strip it, give it a soak in a lye bath. I bought one of those plastic tubs with a lid on it and picked up some lye from the hardware store. Give it a soak in there to dissolve all the gunk and seasoning on it. I've soaked pans as little as a day or two and as long as 3 weeks. It makes cleanup a breeze.
From there you can rinse it off and hit the rust with a mixture of vinegar/water and steel wool. Once it is all cleaned up you can re-season and start cooking.
WSM 22.5", One-Touch 22.5", Redhead 18.5" Smoke Joe Silver, Q200, "Mr. T"