I struggle with this as well. My partner started his first year of med school around the beginning of our second year of dating. He ended up going somewhere relatively near the city we met and lived in (about 1.5 hours away). We saw each other every weekend, sometimes more often. However, I decided to pursue a Master's degree in a city over 1000 miles. I started my program when he started his second year of med school. It was only supposed to be two years, but after 1 year (now the beginning of his third) I decided to pursue two Master's degrees in a total of 3 years. This means we will both graduate in May 2019 (and by that time will have been dating for almost 5 years). He has always been supportive of my decision to go back to school, even when I was thinking about adding on another degree and, therefore, an additional year of long distance.
With the residency match coming up in two months, I have been feeling very anxious and struggling with the same problems you are now.
There is also the added part of me following him wherever he matches that doesn't sit well with me. I try to think of it as like hey- I moved to this city over 1000 miles away for 3 years to pursue my career interests and schooling, and now I am doing what is right for my relationship and my future family, and we are making the rank list decisions together. But at the same time it's like okay sure but really you are just graduating with two Master's degrees and then immediately moving to some totally random place for no other reason besides that is where your boyfriend will be (without your friends/family, job connections, or even an interest in living in that location).
Also lots of people do move simply because their significant other has a job, medical field or not. It isn't unusual or wrong, and it's not like it doesn't make sense for me. I will have graduated/finished the thing I moved here to do, and I always planned on this. But it does make me uneasy - the idea of following my partner wherever sacrificing job connections and opportunities here.