Well, Mark does have something important as an inie in Lumon, if you recall "Mark's freshman fluke" or how that was called. It was some kind of breakthrough with the numbers, which increased productivity to a very considerable degree.
Still, Petey remained department chief.
I suppose they will revisit "Mark's freshman fluke" in episode 8 or (finale) 9.
But no, I don't see how what Milchick did was anything other that super stupid (I just hope it isn't a plot hole). And how he thought it would work out fine if he allowed Dylan back to work. He literally created this mess, without him the inies would have no idea they can switch to their outies without leaving Lumon (and the other way around).
Moreover: how would a super-rich pharmaceutical company only have so few security personnel?
Regarding your point about the possibility that Milchick, Cobell etc are severed (and live continiously in their "inie" form), this is nice and maybe true, but at least Cobell has a backstory (from the Kier cult; also a picture of her when she was young, if real, and supposedly a husband who died).
Would it really make sense to keep someone in inie form indefinitely, instead of indoctrinating them since youth?