Correct me if I'm wrong, but I think I might have actually found a legitimate use case for mapping Nehekhara. Sure, no amount of countermeasures we could gain would help us if Nagash got that level of access to our network. However, that doesn't make said countermeasures useless. It's a whole lot easier to do something a second time than it is the first.
An episode of MASH actually explained this fairly well. For context, a military surgeon is sick and tired of seeing their patients with renal damage dying before they could be transported to the one hospital in Asia with a dialysis machine (although they call it a kidney machine instead). Quote courtesy of IMDB.
Notably, by the end of the episode, they do manage to Macgyver one up, with a little help from the Sear's catalog and a friend with a connection to a Toledo hotdog restaurant (they needed plastic tubing).
Of course, Nagash's methodology can't be found in your local library. Still, if we can reverse-engineer it from the current state of the network, then perhaps some other bad actor can as well. At the very least, I want to be able give a reassuring answer if we are asked by some less-than-trusting VIP, be it an Arch Lector, Imperial nobleman, or Asur diplomat why we think that what happened in Nehekhara won't happen here.