This is actually starting to sound a lot like the argument that was had over telepathy awhile back. Having an army is not that much different that having a power or having a certain set of gear. If people just pay attention to the three cardinal rules of RPing (don't godmod, don't auto-hit, and don't no-sell), a lot of these issues could be avoided.
I'm biased, of course, because I have an army of NPCs. Here's my take, though. I've spent a lot of time on the Abyssal Imperium; in fact, I think I've put more work into it than I have into Nordok. I've gone to great lengths to not be abusive about it, and even announced that anybody is welcome to use Imperium forces in their own RPs or create Imperium characters, because I want it to be a resource for RPing in general. However, I will NOT accept any rule that tells me that I'm not allowed to use my own creation in an RP without ceding control of it to someone else. I didn't stay up all night baking cookies to share with everyone only to be told I'm not allowed to eat any, myself.
I think any ruling should be similar in spirit to the Empire rules. There should be some accountability for being upfront about what kind of forces you're bringing to a particular RP. I've always felt that the key to avoiding confusion and conflict is making sure everybody is all on the same page right from the get-go.
I think an important consideration is the scope of the RP, and the role that the hordes of NPCs will play. Is this going to be a local conflict? A global one? A cosmic one? These all have different standards of what constitutes a "realistic" force. Is the outcome going to be directly impacted by the numbers of NPCs, or are they just there as an obstacle to heroes attempting to get at the villains (or vice versa)?