Whatever you do, any amount of rust on the ways or in the spindle is going to effect accuracy and longevity of the mill. The absolute best solution would be to just replace the table. Next best would be to do some disassembly and cleaning of the entire thing. If there's that much oxidation, there's no telling what other components could be damaged.
Like Steve said, you'll need to hone the ways after you're done, or you can kiss any kind of sub-.1" tolerance goodbye. When cleaning, and especially when blasting WD-40, naval jelly, or any other compounds down onto the ways, you should be mindful that there are going to be electronic bits down in there that probably aren't going to take too kindly to being hit with liquids.