My son took all the AP's in high school but at the advice of his father (EE major), my son took Calculus again as a freshman in college this year instead of testing out of it. He said it IS taught differently and that he is glad he's taking it in college as it is the foundation for the boatload of the math classes towards his ME major. But he said the AP classes in high school have definitely helped with how easy the material has been as a freshman.
As to two sciences in one year in HS - that is a lot. And if her GPA suffers, it could hurt her scholarship chances. And having time to be a kid is important - I think your mom instincts are right about that.
