The DODI 6130.03 is written oddly on this topic. The DODI says a history of RA is DQ. I think the way it'll be applied is history of or current RA is DQ. The Army Regulation and USN MANMED is written such that history of or current RA is DQ.
The thing about "markers" of RA is some of them are non-specific. Other rheumatologic conditions such as lupus, reactive arthritis, ankyloses spondyloarthritis, etc can cause these markers to be "positive." There are markers out there that, if positive, have a high probably of being RA. Was the anti-CCP test used to diagnosis your DD?
A waiver could be possible (never say never), but the symptoms would have to be very mild and not require meds. Also, there must not be any boney pathology on imaging studies. What I just listed isn't an exhaustive list of what will be required in a waiver packet. I'm just giving an idea of the considerations.
I'm not a rheumatologist but what I recall learning about the disease process is you really don't "treat" RA. It's going to progress. You can take meds that can slow progress (btw, these meds are generally not allowed in deployed environments) and alleviate symptoms. Some RA progress faster than others. Some go into remission and flare-up periodically. Being diagnosed at a young age has worse prognosis. It's all these "unknowns" that make the military wary about RA.
Finally, the doctor said "rheumatoid arthritis" and NOT "juvenile rheumatoid arthritis", correct? The latter is a different animal and kids generally outgrow it in adulthood.