The simple, green, answer is: Yes.
Simple Green by itself will not harm rubber (natural or synthetic) for short term washing or immersion (don't leave it overnight!)
BUT: Simple Green plus vibration from the ultrasonic cleaner will dissolve/erode/otherwise damage many synthetic and natural rubbers. If the paint won't come off the seal and o-rings with simple washing or scrubbing with a soft toothbrush, you can put them in the ultrasonic for a few minutes, but I wouldn't leave them for longer unless you have replacements handy.
Be sure to relubricate the o-rings and seals with silicone grease or spray (Regdab Needle Juice will do.) after you clean them.
Micromark has something at a "decent" price?
Not really slamming Micromark, but their prices are usually at the high end of the range. OTOH, you can't beat their service, regardless of the stick you use.