To me, I feel that the Guru is allowing this student to contemplate on his own actions. It could also be that this student will be very harmful to other students if kept near the Guru and the Guru would prefer to minimize the damage rather than allow it to take down the other students with this person. Broken samaya clouds the students' mind and causes them to engage in more and more activities that damages others and they will still see it as benefitting others. If the center has 100 students and this one student creates a lot of schism, distrust, lies, and pit one student against another, create factions or cliques within the sangha community, or does things to distant students away from the Guru, or does things such as misleading the Guru or misleading the student to cause the students to break their samaya to their Guru, obviously the Guru has to do something about it and minimize the damage. He cannot let 99 people's samaya be broken by the force of one person alone. In this instance, the logical solution would be to send this student away so that the student has some space to think about what is going on, or be placed in a situation where he can collect merit to undo the damage done to others.
There are many levels of broken samaya, the worst is when the student does activities that are harmful but yet sees it as beneficial and is completely unaware that he or she has broken their samaya and whatever the Guru says no longer makes an impact in the students mind, or the student becomes sleepy when listening to the Dharma.
This is how i see it, anyway.