Shortly after her installment as Divine, Justinia discreetly began to investigate the treatment of mages by the Chantry. She believed in improving the Circle of Magi, but centuries of Chantry tradition prevented her from simply commanding the templars to follow her vision, which many would resist.
She was wanting to reform independent of all of that.
Fair enough. Still, she has taken her sweet time and that was a big failure, as Master Warder Z says. Ok, I'm with you, looking for reformation per se wasn't a bad move and she has the chance to recover what she lost, but it was a defeat for her slow approach.
In other times, more peaceful times, that approach would have been the right one. Sadly for her, this is the Dragon Agewe're talking about.
Anyway it isn't comparable, the Divine was trying to undermine both factions, She wanted Mages to have more authority and a possible counter to the rite of tranqulity, while at the same time trying to maintain the Templar balance of power, while combating the Lord Seeker at least twice on the management of the White Spire, but her usage of Chantry resources in instigating the escape of Rebel Mages?
Don't forget Lamber had already betrayed her before. Sometimes I wonder if people forget that Lambert ordered Evangeline to kill the mages if they found something in Faramond's research. That was treason, underhanded tactics and conspiration for assassination, yet it's Leliana's part in freeing the mages what should be condemned?