I am past menopause, but "back in the days," I used to get horrible cramping, migraines, and yes--all-over body aches, etc.--all that 'fun' stuff (not!) before and during my period. I was miserable, then one day I heard about
natural progesterone cream.
I checked with my doctor (as anyone should), started using the cream, and it was a huge help for all the miseries. Like night and day, for me anyway!
I have never taken birth control pills, but I do know that there are NFP (Natural Family Planning)-only doctors who would likely be knowledgable about alternatives to BCPs for hormonal issues. I heard someone speak about this topic a few weeks back on the radio, in fact. If you search 'NFP only doctors,' you should find some links.
Good luck!!