I think that the Irminric plot line comes out in the Landsmeet (although I forget). But I was fairly sure that the reason Howe had him was that he was trying to hunt down Jowan. Thus, Loghain wanted him gone to protect his sort of fail!assassin.

As it is, though, the Chantry is pissed off about Irminric being captured as Howe/Loghain/whoever isn't supposed to interfere in the sacred duty of a templar hunting down a maleficar.