Having the same issue. My partner is in medical school around Philadelphia, I got accepted to a few programs 3-7 hours away.
My options are (1) go into a masters program locally and reapply to UPenn, Princeton, etc. in two years or (2) start a PhD program with a fellowship in the fall at a lower quality (still top 25) program. I will most likely take one of the offers and move out. My rationale is that if I wait 1-2 years then she will finish her program before me and we may end up having the identical problem when she looks for residencies, (plus paying 30K for a masters degree and forgoing a fellowship seems like a steep price). If you are both going to be super busy planning weekend trips to see each other and having more alone time during the week may actually not be the worst thing. Regardless, I am very interested in hearing opinions from people who may have already traveled this path. Best of luck and I hope everything works out.
PS Congrats on even being waitlisted at Harvard, very impressive.