My mage found out how he'd have to get the key and realized...this doesn't have a hope in hell of being something I can get away with pulling. Sorry Jowan, I'm throwing you under the bus. Not my favourite origin.
Right? After the first playthrough where I missed that I *could* rat Jowan out to Irving, I always did (a game with more than one resolution to a quest?! Imagine that!). You're in a tower with one exit, guarded by templars. On an island in the middle of a treacherous lake with one boat on it, also guarded by templars. Even if the half-baked plan succeeded without getting caught, where exactly did Jowan think he was going to go anyway?
I never read Lily as being particularly influenced by Jowan. At times it actually seemed like she was the one pushing him to try and escape the tower, telling him that he was up for the Rite of Tranquility and how to get through the magically locked doors. She also knew he was a suspected blood mage and that helping him escape would be a huge betrayal in any case, and then instantly refused to associate with him when it was confirmed that he was.
I'm not saying that she wasn't just a stupid girl who got in over her head, but I'm equally convinced that she was a plant for the Templars who was supposed to get him into trouble so they'd have an excuse to "Tranquilize" him, who then got to take the fall for it blowing up in their faces.
I had a wild hair to do another 3-game playthrough and went with a mage because I wanted to get fired up for a mage Inquisitor. After breaking in to the repository, the PC can say they'd try to escape if only their phylactery hadn't gone to Denerim. Lily tries to encourage the PC to escape anyway because you're smart, unlike her, and you could certainly evade the templars. Except, uh, phylactery? With all the studying and knowledge she's flaunted to that point, she knows that. It raised suspicion and I came searching to see if anyone else had the same notion. I think she's as much a stoolie for the templars as a pragmatic PC is for Irving. It's all just too convenient, and I suspect she wasn't actually punished so much as Greagoir knew he had to have an excuse to get her out of the tower when things blew up.