Maybe she could take the higher science track AND get A's. They are not mutually exclusive, especially in a gifted kid who's highly motivated.
The guidance counselor is right that colleges don't "require" the extra science. But on college applications (including, I believe, the Common Application), the guidance dept. has to rank how rigorous the student's classes were compared to other students ("most rigorous", "rigorous" - something like that). The most selective colleges like to see the highest level of difficulty possible, even if the grade suffers a little. And maybe it wouldn't.
I would go for the harder track if she likes science.
FWIW, at our school, honors classes are weighted 0.5 points, and APs are weighted 1 point. You might want to look into that possibility.
