You could suggest finding a 2 bedroom with a room for you and a room for them.
Sometimes three is a crowd.
People grow apart, and that’s a part of life. Learn to accept it. It still pains me to reflect back on how my high school best friend and I grew apart, he ultra conservative who simply couldn’t tolerate any figment of the tiniest liberal in me or anyone else’s. In the overall scheme of life, none of this really matters as everything in life is transient.
This is part of senior year, IMO. You don’t want them to stay in the bedroom (entirely reasonable on your part) so she has solved problem by moving out. Frankly, lots of leases limit the number of nights you can have a guest stay to prevent couch surfers, etc.
As long as she honors lease and doesn’t leave you hanging for rent, then you have nothing to complain about. Be sure you know where you stand as far as her subletting, etc.
If you still want to be friends, end the apartment stuff as amicably as possible and focus on friendship outside of living together but realize in the short term she may be consumed with BF.
Ultimately you two were going separate ways. You surely do not expect to be in the same city after graduation. It just happened before you were ready for it. It is still the norm for adults to become couples. When this happens there is a shift in who time is spent with. If it had been you who acquired the boyfriend you would have been spending your time with him instead of the girlfriend, regardless of how close you are.
Women have boyfriends who become husbands and are the most significant person in their lives (until children appear) but still retain ties to other women. These lifelong friends are those you can hear nothing from for months, even years, and then pick up with the same intimacy of thought.
Growing up is hard to do. Remember how you left your mother when you first went off to kindergarten, then college? Relationships are dynamic entities. Your mother still loves you just as much as when you lived at home. Your friend still likes you just as much but, like you did, has moved on to a new phase in her life. Use this change as a growth opportunity. Prepare for the finishing of the college phase of your life and the next one.