Thinking outside the box here. Can you make drink joystick covers? Meaning, you put a couple dummy beverages that slip over the joysticks when not in use. When in use, just pull the drink cover off and then you can make the joysticks look however you want. The buttons can just blend in with the tray with a black.
That way you can honor canon and have your own color joystick, and help keep your joysticks dust free.
Thinking off the top of my head, the way I would (try to) make the covers would be to start with real glasses that look star wars accurate, carefully drill holes in the bottoms of the glasses and insert a joystick sized hollow cylinder with a cap into the hole. This will be the area the joystick slips on. Paint the outside of the cylinder whatever color your drink is gonna be. I would probably make it something dark looking, like Guinness colored. Then get some craft water, that gel stuff they use in artificial flower vases to make it look like the fake flowers are really in water. Add dye to make it a dark enough that the cylinder inside is not noticeable and pour it in the glass.
If you want to cover up the buttons as well, you could make a whole control panel cover like this. Permanently attach your fake glasses onto a top overlay panel that slips on top of the control panel. Cut out an empty area on the bottom of the overlay panel to make clearance for buttons. Pull the whole panel off when in use. Then the only thing out of canon is that R2's drink tray will be about 3/4th of an inch thicker. (and I realize it is a complex shaped panel and would be a lot of work to make, but you are the infamous Le Chuck, you can handle it.)