Well, all in all, if Inquisition's account of the war is to be taken into account, the scale of the war is risible. Yes, the Hinterland are a bit ruined, but the only real theaters have been Andoral's reach and the Hinterlands themselves, or so would Bioware make us believe.
I really can't come to believe that a conflict that starts worldwide may be reduced to such localised action. In general, the tone the war was presented at the end of DAII was much more promising that the turn as an introduction pretext for the bad boy that turned to be in DAI.
As for the situation in Kirkwall, I think that the problem (and a possible solution that was not present in Origins and completely left unrecognised in Inquisition) was with the middle ground that the mediating position of the Grand Cleric represents with respect to the circle/order balance of power. In last instance, both of the institutions has to respond to the grand cleric - this can be dificult in practice when the see of the GC is separated from the circle, but theoretically, and practically at least in the case of Kirkwall and Elthina, it was viable.
Going partly off-topic here, I think it would have been quite more useful to Thedas if at the end of Inquisition a puppet or weak, but in any instance, old, divine were chosed to be led by the Inquisition directrices, and both Vivienne, Leliana and Cassandra were made Grand clerics and started their pograms in a lower level, which would have adapted quite better to the varied nature of the regional institution.