Jeanie Bueller spends the entire movie trying to bring her truant brother to justice. In her attempt to prove that her "sick" brother is a big fat faker, she even ditches school herself. She's like the Rick Deckard of Shermer High.
So why does Jeanie bail Ferris out of the jam he's in at the end of the movie? We mean, when Rooney catches Ferris trying to sneak in the back door of Casa de Bueller, he has him dead to rights. Isn't that what Jeanie wants—to see her scheming, universally beloved brother brought down for crimes against attendance?
That may be what she wants at the beginning of the movie, but by the end, Jeanie's grown up a little bit, and it's shifted her priorities. Here's why: First, she listens to the advice of the cute boy in the police station who tells her to stop worrying so much about what her brother does and deal with herself instead. He helps her realize that, sure, her parents may dote on Ferris, but whatever; Jeanie needs to do Jeanie. Thanks, junkie guru.
Secondly, she sees what a hot mess Rooney has become in his dogged pursuit of Ferris. His obsession has left him battered, broken, and thoroughly humiliated. Jeanie sure as heck doesn't want to follow that path. So what's the best way to be the anti-Rooney? Let Ferris escape. Plus, we're willing to bet that he now owes her a pretty sweet favor if and when she needs it.