There is probably a lot of of that--and I have no particular knowledge here--but my guess is that, in addition to trusting Freeman:
1) The school was a bit anti-football during the Pres. Malloy era and saw the program as in direct tension with ND's academic ambitions: to be an elite ivy-like school. Under Jenkins, ND began transitioning to a more corporate/brand-focued model. During that perod, the football program gained back a lot of favor during as it was clearly a profit center and a driver of the brand. Anecdotally, you can see this transition in the return of the classical architecture.
2) During the same period, higher-ed turned away from strict academics and a score-focused approach and became much more willing to let in kids with different academic profiles. In fact, the elite schools became kind of fixated on making non-sport admission exceptions. So even though the school got harder to get into during that period, it was not adverse to diverging from its typical profile. Doing so was seen as a positive, not a negative, if the kid could hack it. As long as they are recruiting the right kids, the football players are seen as future community leaders more than subpar students.