The three Pope options were her, Leliana and Cassandra. She was probably the least popular so it kind of makes sense to give her that ending. Leliana had the most revolutionary one where she freed the mages and allowed them to govern themselves, which ended up causing lots of conflict.

Cassandra had the centrist option of making the mages cops partnered alongside the Templars (instead of their prisoners) and that fixed most things.

Templars wanted to eat rocks and kill all mages, mages wanted to not be killed?

Pretty much.