Because Captain Pike decided, for better or worse, to give them a break.

As he is portrayed in the Abrams-era films, Captain Pike is a firm but nice guy. If "Cupcake" (as he has come to be known) and the other cadets had a note in their records saying that they beat an unarmed civilian to a pulp for no apparent reason, they might have a tough time finding future assignments, and that's assuming they aren't thrown out of the Academy itself.

Pike gave them a second chance. This is a behaviour that Pike displayed with regards to Kirk himself several times in both Abrams-era films.