If the lathe is working perfectly, the rust in the "ways" is your least of worries, you have various way to deal with it, my way would be to "kill" the rust by wire brushing the rusted area, clean with acetone (make sure the acetone doesn't run into the paint) and the brush the rust with any of the rust inhibitors products, available in the market. Any auto parts store and hardware stores will have it.
After the "rust killer" has dried or done its job (look for the product specifications, for that.), grab a small block of wood and wrap some wet and dry sandpaper 600 grit would be OK and then run it on the ways, as if you were shaving a piece of wood with a hand plane, you want to "flatten" the area treated but not remove much good metal surface and the 600grit with plenty of water, will do a good job on that.
After that is done, you only need to maintain the area lubricated (WD40) as you would if the rusted area was never there...!
Good luck...!
Cheers
George