This is an age-old dilemma. Kicking children out of yeshivas is different to not allowing them in in the first place. I am absolutely, incontrovertibly NOT saying that anybody who comes from a Baal Teshuva house should not be allowed into frum schools. What I am saying is that a careful judgement must be made of who to accept into the schools, and if needs be, open another way. Why should one family’s careful chinuch be thrown down the drain by one friend who wasn’t privileged with the same? (I have personally seen heimishe boys being dragged down terribly by people who should never have been in the school in the first place) It isn’t about the history of the parents, it is about the standards of the family. If the family keep the school’s standards, then they should be allowed in. If they don’t, it doesn’t matter what other good things they do and how far they have come; their kids don’t belong in the mosdos.
Obviously, this is subject that needs Daas Torah to decide. There are conflicting sources for this in the Torah. (eg Dinah marrying Eisav; R’ Yossi ben Kisma; Yackov travelling with Eisav…), and it isn’t for any of us to decide. But I can tell you many stories from personal experience how one child brought down so many others, when he should have simply been refused entry and put into another school which was more suitable.