Well, after having it pointed out to me that Codex: Witch Hunters does in face explicity state that the Adepta Sororitas act as the Chamber Militant of the Ordo Hereticus (pages two and six), this got me thinking; Does this mean that the Adepta Sororitas ARE actually part of the Inquisition?
I think not, I will explain why below. But what do other people think?
First, the fluff state that the Adepta Sororitas agree to act as the Chamber Militant of the organisation, when called on to do so by a duly appointed Inquisitor. This to me indicates that the Inquisition still have to ask, which means the Adepta Sororitas can refuse (whether they choose to exercisethis right is irrelevent). This is not the actions of a subordinate part of the same organisation.
Second, this arrangement seems to be simply a more formalised form of the usual Imperial procedure which allows an Inquisitor to requisition whatever forces he deems necessary, up to and including entire planets.
Third, the fluff goes on to state that the Adepta Sororitas remain under the auspices of the Ecclesiarchy and retain the responsibilities given to them by Sebastian Thor. This seems to me to indicate the original agenda still stands alongside that of the Ordo Hereticus and that at an institutional and administrative level the Adepta Sororitas are NOT part of the Inquisition.
Fourth, in theory at least like any treaty the Convocation of Nephilim could be revoked, meaning the Adepta Sororitas would cease to be the militant wing of the Ordo Hereticus. No indication is ever given that the Grey Knights or Deathwatch could ever split from their respective Ordos.
To sum up, I think that while the Adepta Sororitas are the Chamber Militant of the Ordo Hereticus, they are not part of that institution and could cease to be the Chamber Militant by revoking the Convocation of Nephilim