Short of tearing completely off your roof & taking a shingle or two along with some under-shielding paper I don't see it doing any damage to your roof due to wind. Even if it wasn't done to code by hitting a stud or other roof support I doubt it would blow off. If he wants it moved, I would guess somewhere in the $75 to $100 area along with the price of the pole (which I've seen included in some areas & charged for in others). You could also attempt to mount your own pole & aim the dish yourself if you have some experience with this type of thing. Don't forget to seal up the old holes where the dish used to be located or your landlord might be having water issues down the line.
edit: The Protection Plan doesn't cover these types of moves.
