NOTE: Major Rook is a secret agent and is treating this matter professionally as his duty to the crown. He feels that the group is in way over their head at this point and wants to get help *immediately*. In particular, he feels like he has a sword hanging over his own head (the deal with the Beast) and wants to leave something behind for his replacement.
I think we are dealing with a number of issues here. I am quite familiar with the hierarchical cell structure you mention. One has a central headquarters at the top, and they hire controllers who are well-placed. A controller basically does nothing to break their cover except give orders to agents and transmit information back to HQ. If captured, they don't know anything except their own agents. The mobile agents may be getting into trouble, and may hire footmen (who know nothing except the agent who hired them).
The problem with this model as applied to us is that our Company are at the bottom of this hierarchy. Edwards, Woodhull, and Stringham are all extremely exposed -- and myself and Mr. Eck only slightly less so. If trouble hits, it will most likely be through us, not through some flunky of ours. For example, Fu Manchu would have to be blind not to know where Edwards lives at this point. If we mess with him, it is quite conceivable that he could just kill us all when we meet at Edward's house.
What can we do about this? I will offer a few suggestions:
I have not seen anything in either of them to indicate that they are untrustworthy. They showed fairly honest dealing with regard to the affair with Milverton, and I think some competence in finding his lair in Rotherhithe. As for the grave-robbing affair -- we're hardly in a position to judge them on that count. They are not particularly knowledgible regarding the supernatural -- but they are no less clueless than we were two months ago, and their magic produced the mystic connection to us (via ``etheric waves'') on its own.
Edwards judged that Mathers seemed power-hungry in his setting up the society. I see his motivation as somewhat self-aggrandizing, but also scholarly and creative. Certainly he doesn't seem like the type to become an evil or criminal mastermind -- he's a respectable mason, working on becoming married, etc. However, I will defer a more thorough check of his background.
This is the closest we can come to a cell scheme, I think, unless Edwards, Violet, and Stringham are willing to completely abandon their lives and take on new identities (which they are not).