If you want my serious recommendation it would be to have a sit-down with your department head, and any other faculty in your program, and ask them their opinion as to a path through a linguistics degree, particularly an advanced one, without phonetic transcription being a big part of it.
I have to believe there is a path through, though I would imagine it would involve a specifically designed undergraduate path as well as a clear idea as to what your graduate focus will be and that it not involve phonetics (transcription directly, not an understanding of, which of course you'll have).
They are in a far better place to give you informed opinion, and the direct assistance with program design that you'll need, than I can. There's nothing wrong with reasonable accommodations in academic pursuit, particularly if your desired area of specialty does not rely on an area of study that's not essential to it in any meaningful sense.
Brian - Windows 10 Home, 64-Bit, Version 1809, Build 17763
A great deal of intelligence can be invested in ignorance when the need for illusion is deep.
~ Saul Bellow, To Jerusalem and Back