Is she the kind that would likely go on to grad school after? If so, BYU is great preparation for that as it is one of the top schools in terms of students who go on to do a PhD. There's a lot of support built-in for undergraduate research at BYU. At a lot of the top universities (and even not top universities), a lot of the professors focus more on graduate research. And so getting undergraduate research positions can be more competitive at those places. Given her academics, she'd easily get a research position at BYU which she could leverage to get into a top school at the graduate level. When applying for graduate school, research experience will generally stand out more than which university you went to for your undergraduate. This would also generally be a cheaper option.

Now if she wants to get into a big tech company or get into the startup culture right after graduating, then she's probably better off going to a top school.

Still given all of this, it may not hurt to apply to a few top places and see what sales pitch they can make. Regarding church stuff, others have commented on this. For what it's worth, BYU seems to be getting infected with a lot of the things that plague higher education as well. It will probably be worse at other schools, but perhaps she thrives more by being in the minority.