I've been reading up on the Prussian Crusade (mostly in the context of the Teutonic Order), and it seems like a great setting for a saga! You've got a large conflict going on, with magi doing their best to avoid getting sucked in, and you've got a point of intersection between the faerie/magic aligned pagans and the dominion. The varying motivations of the crusaders themselves, from military experience to salvation, as well as the brutal response of many of the natives, would make great moral fodder for characters to obsess over. Thoughts?
There is a saga setting in Guardians of the Forests (the Rhine tribunal sourcebook) that describes exactly what you are talking about 
IMO yes, it is a cool setting for a war-based campaign. And not only about avoiding it, but also about underhand attacks and real massacres performed by the magi. Remember that the order only punishes you for being caught meddling with mundanes 
Cheers!
Xavi
I was unaware of the existence of this book, it will be my next purchase.
Heh, so long as their wrath does not fall on your sodales, mess with them all you want! Just make sure the Quaesitore doesn't notice. 
The Daragon and the Bear the Novograd tribunal source book for 4th ed covered this area giving some useful information. (e23.sjgames.com/item.html?id=AG0260)
I also found the Osprey books series on the castles of the Teutonic order useful as it included pictures and floor plans of some of the castles that are /will be in the area