I'm fairly certain my fluff knowledge isn't quite as in-depth as yours, Lynata, and not to take away from your (in my opinion valid) points in the other thread, but my understanding of Grey Knights were that they were nearly as far above "line" Space Marines (everyone but a HQ or a Special character in tabletop, basically) as "line" Space Marines are above the more elite humans.
There's definitively some truth to that, but given that we're likely talking Ascension level here I think it could well be that high-ranking DH characters can hold up to "rank and file" Grey Knights in the same way as a HQ Inquisitor can accompany a bunch of GKs on the Tabletop (or in some novels). I mean, Ordo Malleus Inquisitors can even wear Terminator Armour ...
Basically providing rules for 1-4 Ranks of Grey Knights that are somewhat comparable to experienced Ascension characters with appropriate equipment. The biggest difference from DW would be that their weapons are actually balanced to work by the same damage scale just like they do in the fluff and on the TT. At least that'd be my idea on how to tackle this.
Providing fewer Advancement Schemes for the GKs would also allow them to fit in easier in terms of page count, in addition to balancing (limiting) them to the range of other characters.
For me what's interesting is how Black Crusade will interact with the Dark Heresy Daemonhunter book. There's the risk of some overlap there.
I'm interested to see this interaction as well, but also because both books will be new in that they actively try to have "normal" people work alongside Marines instead of creating different "power levels" as it happened with DH/RT <-> DW.
I believe the general assumption is that instead of deploying 1,000 guardsman, you would instead deploy 20 Marines, or 5 Deathwatch marines, or 1 Grey Knight.
Who still is not invincible, mind you. 1.000 Guardsmen likely bring a lot of heavy weapons and armoured vehicles along. It's not as if they'd just line up with a bunch of lasguns and wait to get slaughtered. But even then we've heard of enough cases where lasgun shots have felled a Marine (despite it not being possible in DW unless you use Horde rules).