In the end, the academy agreed to join the Holy War on the side of the Followers of the God of Fate, but the condition was that no one was forced to participate regardless if they were normal people living in the city or students of the academy.
Gregor didn't have any issues with the condition since he never planned to make ordinary people join him. It was usually the people that filled with hatred joined the Followers of the God of Fate to obtain revenge after having suffered in the hands of the Cult of the Goddess.
He was interested in experts of high Rank because, at the end of the war, those experts were the ones that would mark a difference. The weaklings, even if they were reinforced by swearing loyalty to him, would just be cannon fodder.
Of course, the matter of the academy agreeing to side with the Followers of the God of Fate was kept secret.
