Squeezing the piston out and cleaning it from the outside is fine but only when you know it's all good on the inside.
My guess is once you've done a caliper overhaul it will all work fine again.
Just use a fair amount of Red Rubber grease on reassembly, then give the piston a spruce up with Brake Cleaner and a toothbrush once or twice a year, then more Red Rubber grease on the outer pistons and chances are it will behave itself in future.
Personally I've always avoided organic brake pads as well as the dust can cause most issues, I've been using ceramic pads on the rear to keep the dust down which definitely helps.
The alternative is to change it for an FZS 1000 rear caliper as a lot of people have done which requires less maintenance, but if you don't mind keeping yours in good shape with an occasional bit of TLC then it will work just fine.