Can you check out the school first? That might give you a better idea of how a non-Catholic might integrate into the school.
I have kids in Catholic High School and elementary school. In both schools, all students are required to go to and participate at Mass (non-Catholics get a blessing instead of Communion at Mass), participate in the daily prayers and take part in other school functions such as the living Rosary, the May Crowning, etc.
Even if the parents are anti-Catholic, this doesn’t mean the student is or that a strong Catholic education won’t be good for her. You are writing a recommendation for the student; not the parents so just state truthfully what you know about him/her in terms of academics, service, whatever else they ask about.
Unlike the public schools, Catholic schools don’t have to put up with parents who try to tear down the faith. If their actions are anti-Catholic, they will be asked to leave. And there is a strong likelihood that, in spite of what you may have heard, that the family isn’t all that anti-Catholic or they probably wouldn’t have applied there.