You could do that, or if there is a gap between the cover and the baseplate you could gently pry it off. Either was you will be peening/swaging the pins down when you put the cover back on. A longer term solution for the cover is the grind off the pins and drill/tap holes for small machine screws to hold the cover on. You will also have to countersink the back side of the backplates so that the screws will sit flush with the plate. Or, you could make"divots" in the headstock to accommodate round/pan head screws, similar to how old Ricks and Fenders had "divots" for the old Kluson tuning keys.