This isn't the first time the inquisition's been shown attacking the grey wardens, the fire's above trailer, one of the game informer videos, and this one. It could be due to any number of reasons like Coreypheus, the first warden targeting the Anderfels kingship and making up rumours about a blight, farming red lyrium, working with the antagonist etc or it could be a combination of many different things or factors like us deciding to attack them if we have a choice in the matter.
The last flight should shed some light on it combined with the grey warden companion, the fact we can investigate pretty much everyone we may learn some really dark secrets about them.
As for where, there's a couple of fortresses in Orlais, Adamant which was in Asunder and shown in one of the game informer videos or Montsimnard which has some ties to a lot of thing's like the masked empire, Vivienne, where Loghain was sent, some of the other books, where the head quarters of the orlesan wardens are, Jader, or the ones in Fereldan, Vigils keep, Soldiers peak.
Who knows, it's hard to tell at this point.