And of course the black wires wouldn't be marked on the "call before digging" maps, since they have to be completely secret.

Sad thing is, given the nature of intelligence ops, I just can't think of a better way to handle it than "let them dig, but scare the crap out of them if they hit anything." Even marking the lines as something else would give their location away; you can bet that every other government in the world is doing their damndest to find every single sewer pipe, A/C condiut, and water line running into or out of the CIA, just on the slightest chance it may help them penetrate the organization.