The Academy didn't protect Elias from outside influence because they cared about him. Instead, it was simply because Elias was their ticket to get more concessions from Chronos.
The Delegation from Chronos wanted Elias to participate. In return, they have agreed to give the Academy more slots. The Academy shouldn't refuse such a lucrative offer.
As they had accepted the offer from Chronos, they couldn't let anything happen to Elias before the designated time. Even if Elias was to die, he had to die at the hands of those from Chronos.
If that happened, then the Ashborn Family and Chronos were going to have an even bigger conflict. This was beneficial for the Academy from every angle.
To protect their interests, they had decided to protect Elias until the promised time. After he left the Academy with the Chronos delegation, then his fate had nothing to do with the Academy.
Even if the Academy was supreme, they couldn't dare to hurt Elias if his father wanted to protect him.
