White vinegar isn't bad for rubber parts, it's only damaging to SOFT rubber--i.e. joker valve--when left to sit and soak in it. So you don't want to leave it sitting in the bowl. However, you DO want to flush a cupful ALL the way through the system once a week to dissolve mineral buildup in the head discharge hose, and yes, the joker valve too. Follow it with a fresh water flush after an hour.

To prevent a buildup in the bowl, spray it with white vinegar once a week. After an hour, rinse what hasn't already evaporated with a quart of fresh water.

Or, tee your head intake line into the head sink drain line to provide a source of clean fresh water (do NOT use gray water for toilet flushing!) to flush your toilet once a day.

Notice that you asked how to REMOVE scale...I've told you how to PREVENT it. Prevention is always cheaper and easier than cure. However, increasing the frequency of vinegar applications to daily for a week or two will remove it...then you can start preventing.

And speaking of the joker valve, it should be replaced annually in a manual toilet anyway. Vic Willman at Raritan sent this to me...it explains why:

JOKER VALVE 101

Most people think that the only thing the joker valve does is acts as a check valve to stop backflow from returning to the toilet or odor from the tank from escaping through the toilet. But that's not a joker valve's most important function...in fact, the joker valve is THE single most important replaceable part in a manual toilet.

Here’s how the discharge half of the pump works: On the upstroke of the piston, a vacuum is created in the area beneath the piston. This causes the joker valve to close tightly, and the flapper valve beneath the pump to open, allowing some of the contents of the toilet bowl to be drawn into the bottom half of the pump. Then, on the down stroke of the piston, the flapper valve is slammed shut, and the effluent is forced out of the bottom of the pump, through the joker valve, and off down the line. But when the joker valve becomes worn and/or there's a buildup of sea water minerals on it, it can no longer seal tightly on the upstroke of the piston...less vacuum is generated when you pump it. And as it becomes more worn less and less vacuum, till finally the bowl contents simply move up and down a bit, but don't go anywhere. Sometimes the flapper valve needs to be replaced too, which is why toilets should also be rebuilt at least every 5-6 years as PREVENTIVE MAINTENANCE.

You prob'ly won't notice the loss of efficiency at first because it's so gradual...same as we don't see that we've gotten a little older than we were yesterday when we look in the mirror each morning. But I guarantee you that if it's been two years or longer since you replaced the joker valve, you need to pump the toilet at least 50% more times to move the bowl contents to the tank or all the way out the thru-hull....IF they're getting there at all any more.

Marine toilets have moving parts that require maintenance. PREVENTIVE maintenance is called that because it PREVENTS problems that have to be fixed. You get to do PREVENTIVE maintenance on YOUR terms, when it's convenient for YOU...unlike repairs, which NEVER are needed at a convenient time.