IIRC Leliana offered no advice to Justinia on an alternative method of freeing the mages from the Temps and did just as she ordered, even when common sense dictates that warring against your own military arm will only make the situation worse. Plus her being a spymaster means jack when it's mostly used in service to her master, autonomy be darned. From what little parts she's had in Asunder and TME she seems like stooge. I wouldn't be surprised if she aggressively pushes for the Chantry's agenda on the Inquisition.
I would be surprised if she actively pushes the Chantry's agenda, as she expresses her dislike of the Chantry's beliefs in Origins. There's also the very high probability that Justinia dies in the Fade Breach at the start, meaning that Leliana would have no connection to the Chantry anymore.
Just real quick I wanna freshen up on something. How did bioware say Leliana survived if you chopped off her head? I remember Gaider saying that if you killed wynne Asunder would unfold differently but am unable to remember why Leliana was always alive. I know they answered it. Sorry if its off topic I just can't remember if the answer was Maker or not, and its probably best to ask in a Leliana thread and not create a new one for so simple a question.
The actual decapitation didn't happen, that was just a gameplay effect. You stabbed her and left her for dead in the same room as something that managed to heal Arl Eamon from some sort of demonic sickness. It's rather probable that she survived.