I don't understand why the Defence Dept is so precious about Pearce? If Darwin can be a combined civilian/military airport, why not Pearce??
Because they are allowed to be by their political masters. Every time a new defence minister tries to wield some authority over defence it ends badly for them.
http://en.wikipedia.org/wiki/Joel_Fitzgibbon
Not only Darwin. Townsville is joint user and so is Richmond to a lesser degree. Air traffic is traffic, all can be managed. As for "special military requirements" that is what training areas and PRDs are for.