My kid also chose music theory over a core class and did well with admissions. They made that choice based on interest and a desire to enhance other music studies outside of school.
Make sure your daughter submits a music resume if appropriate and if schools accept them: recording/video, music resume, and a letter or two of recommendation related to music. Music achievements can often help with admissions. The guidance counselor can also write a note explaining the choice of music theory over French if it is still a concern. Colleges, even top ones, understand commitment to music.
Music majors have a relatively high med school acceptance rate. If prerequisites are not covered during college there are many post-bacc programs for that purpose, some of which may help get into the med school that hosts the post-bacc. But those programs do cost.
One other idea: she could also take French- or music theory- online. Our small school had scheduling issues and so my kids took online classes a couple of times at VHS Learning | Home (We eventually suggested our high school join this organization so that 25 students could take an online class per semester.)
And good for her for choosing based on her authentic interests!