Under normal circumstances, it's not unsafe to not have a period. However, the hormonal imbalance that causes it from PCOS puts us at increased risk of other issues, namely endometriosis and uterine cancer. This is because our body doesn't just stop our period due to environmental stress (as what happens with athlete amenorrhea), but rather, the state of amenorrhea is dysfunctional and incomplete. We do still go through the cycle, and depending on your hormone levels, you still go through the endometrial lining stage (this incomplete cycling is why we get cysts -- they're underdeveloped eggs that didn't make it to the release stage). Combined with the estrogen dominance, this can alter the endometrial cells and potentially lead to cancer. In the shorter term, estrogen dominance can hinder weight loss and prompt testosterone levels to increase, leading to the classic acne, thinning head hair, and excess hair in other places symptoms of PCOS.

Prometrium is a synthetic progesterone hormone, so taking it will help reduce your estrogren dominance (though I do hope that your doctor tested your estrogen and progesterone levels). Yes, that means you'll get your period back.

It seems odd to me that he then prescribed birth control. What birth control did he prescribe? If it's the standard Pill (Loestrin), then I'd think that kind of defeats the purpose of prescribing the progesterone, because Loestrin is an estrogen-based birth control.