Well, that's odd as GPS was created by the US department of Defense. You would think that guiding ballistic missiles was just the purpose they had in mind.
GPS, although accessible to civilians since Reagan's order following KAL-007, wasn't ubiquitously useful until 2000. The DOD intentionally degraded the GPS signal so that (theoretically) only the U.S. military had access to accurate GPS. Clinton ordered this policy (Selective Availability) turned off in 2000, as the DOD had developed other methods of denying GPS on a regional basis, and civilian technology was beginning to develop workarounds anyway. (Which is why Russia / China are actively launching their own "GPS" satellites.)
In other words, it is not unprecedented to have a separate "civilian GPS" and "military GPS". The relevant rule is that all U.S. GPS receivers for export must either a) shut off above 11km in altitude and 515 m/s; or b) be classified as a weapon requiring a State Department export license.