It sounds like the doctor's comments were based on two things. First, her conception of homeschooling may include the notion that it's negative regarding the child's socialization (this is a common idea about homeschooling that is sometimes a total misconception, but she may feel more justified in holding it due to the smaller local population, especially if everyone else puts their children in school during the day). Second, she may feel that you are overly stressed out over your daughter's intellect and education, and may feel that instead of putting so much focus on that, you yourself would be better served by turning your focus a bit elsewhere, especially if she links your interests to the migraines (hence the "alone time" comment).
She can't be faulted for holding her opinions, but you and she seem to have different boundaries for what's acceptable during a doctor's visit. I think that master of none's advice is spot on. You can make a deflecting and noncommittal sort of response, but if you don't want your doctor making such comments, knowing now how she feels, you might try explicitly setting some boundaries with her. Even if you're friends outside of the office, you can gently tell her that you'd like to keep your doctor's visits focused just on medical issues regarding your own care. Another thing to try is to put less information about your daughter "out there", at least with this particular person, which would make it less easy to bring up in conversation. She might still try to sneak in a comment or two, but if so, I don't know what you can do besides try to switch doctors, which might be difficult due to where you live.
