The Puffs break into the Headmaster’s Office as part of their initiation ceremony into the Puffs, and also seems to serve as a hazing ritual at the same time, as it’s the sort of harmless prank that inductees to a secret society might have to go through to prove their sincerity. It’s very mild compared some of the things real sororities get up to, but has the same cult-like feel.
The Puffs seem to have been doing this ritual for at least fifty years without ever being caught or reprimanded, so it makes you wonder how Rory got so unlucky that Headmaster Charleston will very soon come in and bust them. Presumably it was common practice to turn a blind eye to the Puffs and their activities. The only thing that could explain it is if Headmaster Charleston is relatively new to the job, and has decided to crack down on sororities at school.