The federal troops stationed at Fort Douglas during the Utah war were sent explicitly to depose Young as territorial governor. John Rocky Park, president of the University of Deseret, moved the entire school from it’s temple square adjacent location into the grounds of the occupying army and declared the university a secular institution.

The church/territorial government (there was no difference- hence the Utah War), under the direction of Young, cut off all funding to the school. Young not only wished the school didn’t exist, he attempted to make it not exist. That was the sequence of events that prompted the formation of a second church school- BYU.

So that was the price the Universiity of Deseret/Utah paid for its academic freedom. And that is why Utah is in the PAC and not BYU.