Yo I could totally see Jowan replacing Anders' role in DA:2. Honestly, it fits so much more. Not questioning the decisions by BioWare, but honestly I really dig it.
He was already always so keen on screwing everything up, and after seeing the manipulation of mages throughout his life: the dis-ownership of his father/family, the order by the circle to make him tranquil, the separation of him and the love of his life Lilly, the manipulation of a Teyrn to forsake Jowan, etc etc.
If you think about it...all those events really could shape Jowan in being a more suitable personality for DA:2 "Anders" than...well Anders.
Anders was a hilarious badass in Awakening. Totally pulled a 180 on his character in DA:2. The whole "Justice" explanation is whatever, it didn't fit and I never got over it. I'm sure there are others who feel this way.
Basically my point is Jowan has been exposed to the cruel life of a Mage just as much as anyone could expect. It was SO possible for Jowan to fill Anders' role in DA:2. No Justice story needed. Jowan is just a guy who acts with his emotions, I think we could all see him blowing up the Chantry.
EDIT: Also, when Gaider said most players would percieve Jowan as "oh, you mean that guy in the middle of DA:Origins? I call bullsh*t. At least EVERY player meets Jowan. No matter what. Sure, Mage Wardens have a deeper backstory with him, but RedCliffe castle is NOT optional, therefore you must meet him. However, both Isabela and Merrill can be totally missed. And both were incorporated as companions. So yeah!