I'm an Air Traffic Controller in the Air Force and I've just been diagnosed with Lupus. Will i be kicked out?

Why would you think that they would kick you out? They might only if begins to affect your work. The best thing to do is to be honest with them about your diagnosis. If you tell them, they will be easier to work with. If they find out from someone else, you may get fired for withholding information. Just tell them.