Hmm, I think that the DH could be filled out quite a lot. It just takes a bit more creativety to expand on the fluff.
I see the name irratates people as much as the notion of C: SoB & C: I irratate me. I guess too there's some consensus here that the codecies have to fit in with Imperial Hierarchy. They don't.
First to what you've said about GKs. GKs may not have the manpower of the Eccleciarchy but the Grey Knights in total are more numerous than all but a couple of the Space Marine Chapters (Ultras & SW, I think?)
Secondly - for their role in the Imperium. Let's not forget that the SoB's aren't really a force built to fight full xeno armies but more bands of mutants and heretics within the Imperium - a specialist area too. Yes there are incidences where they've fought Orks, Necrons etc, but I bet they weren't situations where command called them into to do the work and that they were more likely caught in the middle of the situation or more readily available then the nearest SM or Guard army. Unless it's an internal uprising, I bet 9/10 those two armies are the only ones considered for the role of taking out xeno incursions.
Just wouldn't knock the role of daemonic incursion just because it isn't as widespread as heresy.
In any case, I just don't see GW binding the codex just because of fluff-to-army size as you've suggested. If scale and use of forces mattered we'd have several codicies for Imperieal Guard armies such as Cadia et al and not the half dozen SM codieces we have currently. No they prove that it will be on popularity and sales. The bottom line - GW are a company. GKs are nearly as popular as SoB and as I've said before alot of DH players play pure GK armies - as much as SoB players do I'd say.
I don't want to totally blank out Inquisitors as there is a high interest there and I would interested to learn more about it too on both sides. It's just that a lot of issues I read from DH players tends to focus the GK side rather than the overall Inqusition side and that I bet most DH players would like a larger GK focus, considering that the DH codex is largely Inquisitor focused (IMO). My vote goes like this, as GW love their themes - We'll get either;
C: GK & C: SoB
or
C: E (Eccleciarchy) & C: I (Inquisition)
or
C: IA (Imperial Agencies [Combined])
I guess what this rattles down to is getting slightly OCDC about the titling. I do like the second one best as I'm guessing most would but the name suggests it excludes Inquisitors from the SoB force. I just doubt it will happen as there are handfuls of WH players who like Inquisitors too. Hence why I think it would be best to go with the former titles as Inquisitors are known to co-operate meticulously in the issues of both forces but with actually being part of the army itself.