If the Inquisitor sided with the mages...
I've seen the transformations. It's a horror to watch your soldiers' faces change, to realize they might not remember you day-to-day; it's a sword in the guts. But the ones who make it through are near invincible.
Feed elfroot to the soldiers hurting, as much as they want. Beyond that, it's just waiting until they stop feeling pain. Remind them they spread the lyrium. It grows at our touch; with the "materials" I've sent, they'll grow enough for a dozen armies. It's proof we're on the right path, that any suffering is worthwhile. Remind them.
If the Inquisitor sided with the Templars...
My fellow captains:
You know as well as I do that we can't cut back on the red lyrium we're feeding the soldiers. Considering how many knights we lost in our failure at Therinfal, we're lucky the Master still has a use for us. If He demands a small army of red templars, we will deliver.