Note that RJBS was not responsible for everything that was done at YU. He did not even start there – he first negotiated a partnership with YU when his father was the Rav there and RJBS had a yeshiva in Boston.
One example is his article about opening of YU Medical school. He said that many people asked him – why is YU going into this business when it was first formed on donations for a rabbinical college. He then says that he can justify it b’dieved – because he was not consulted about this l’hathila! His justification is that Jewish community suffer from non-religious doctors (it was that way in Lita) who are not sensitive to religious patients (it is easier for me to talk about these issues with non-Jewish doctors than with non-religious Jewish doctors). So, if some doctors will go to YU – they will not necessarily become observant, but at least they will have sensitivity to halakha and hopefully will be better for religious Jews.