I didn't let her kill the agent at the beginning. I just did her personal quest and had a whole dialogue with her about her losing herself, first as a bard and then as the left hand of the Divine. She took Justinia's note as release from her duties, and an apology. She seems pretty intent on separating herself from the Chantry at an official level and just being Leliana again. To the point where I asked her if she was going to leave me.
She said not until this Inquisition is finished, but that she does want to leave when this is over. She seems to want exactly nothing to do with being Divine at this point, while Cassandra seems pretty down with the idea (if needing a confidence boost) in the convos I've had with her.
If she ends up Divine at this point I'll be pretty pissed because she clearly doesn't want it at all. I'm interested to hear how her attitude differs in other playthroughs since it seems like a lot of people are getting a different Leliana.
Also worth a note: I told the Chantry representative that it was Cassandra and Leliana's decision.