Well, Inquisition revolves a lot around Machiavellian ideas. In this context, power play could very well lead to a situation where templars could be forced to submit to an Inquisition led by an openly practising blood mage (not that I'd consider that to be all that great an idea, because if just the companions know about the Inquisitor being a blood mage, it's quite enough, no need to spread it around. Just need to make sure there are no witnesses
).
- Paint an overwhelming threat bigger than blood magic (check: Corypheus)
- Apply military pressure (check: beat templars and their boss)
- Offer them a way out to tackle bigger threat, but under extremely close supervision (dissolve their order).
- If necessary, establish reign of terror to weed out dissenters, and to keep the rest from getting uppity.
Edit: Oh, and make plans for when the external threat (Corypheles) is gone. Because stuff is going to get pretty bad pretty fast then.
Besides, it's not as if Blood Magic can really make things much worse. Large parts of the population already believe the Inquisitor to be the killer of the Divine, despite all efforts to paint him/her as the Herald of Andraste. Considering how that alone would merit a death sentence for the Inquisitor, and outlaw the entire organisation, blood magic would just be a drop in the bucket.