you should wash off the stones every time you do a water change

one way to stop the algae is to block the light with maybe a decorative pot, this should at least slow it down if not stop it out right. prevention of is better than reaction to, not to take away from Christine's advise. Maybe step up the water change frequency too.

Could you pot it in some proper substrate or change over to semi-hydro. That's the idea, right there! Have you looked up the Vermont Hoyas videos on semi-hydro? I think you'd be much happier than with the current set up.