I don't think integrating it will be difficult.
The Inquisitor is the head of a massive organization who often sends out agents into the field. You'll probably play one of those agents. You can get simple objective like 'Clear this castle of Avvar barbarians.' 'Defend this mine from undead.' 'Explore this ancient elven ruin.'
Yep.
The story lends itself well to co-operative MP, in a way that DA:O or DA2 never did. It almost seems designed that way.
An organisation full of operatives and soldiers from all races, nationalities, allegiances and causes, fighting evil to spread the influence and power of the Inquisition. There are four enemy factions (at least) aligned against the Inquisition, and the geographic scope of the story allows for a huge and diverse range of maps, quests, experiences, etc.
It's basically as good a setup as ME3's war against the Reapers/Cerberus, and I didn't find anybody calling that absurd or nonsensical.