As far back as 1982, the Pentagon was looking to establish its own presence in space, independent of NASA:
"Looking toward the day when they will be directing their own missions, teams of Air Force officers are working as observers at the Kennedy Space Center in Florida and the Johnson Space Center in Houston. The lessons they learn will be applied to operations of the military’s own shuttle launching and landing facilities, which are under construction at Vandenberg Air Force Base, Calif., and expected to be ready in 1985. Officers will eventually assume control of military shuttle flights, working out of the Consolidated Space Operations Center that is to be built near Colorado Springs, Colo. Meanwhile, the firing rooms at Cape Canaveral and Mission Control at Houston are being modified, at a cost of $26 million and $47 million, respectively, to provide security for military missions.
General Abrahamson said that the partnership between NASA and the Pentagon ‘‘is being strengthened’’ and ‘‘will prevail in the operation of the national space transportation system for the foreseeable future.’’ The Reagan Administration, in a space policy statement released at the time of Columbia’s landing last Sunday, also emphasized that ‘‘close coordination, cooperation and information exchange’’ will be maintained by the civilian and military space programs. NASA will continue to have overall responsibility for the shuttles - a fleet of at least four is planned - and to maintain operational control of all scientific, commercial and other civilian missions. The Defense Department will control all military missions, which include the deployment of reconnaissance satellites and the testing of antisatellite devices to ‘‘deny any adversary the use of space-based systems to provide support to hostile military forces.’’
But the Administration said that in time the institutional structure for the shuttle fleet might change. Consideration has been given to turning over civilian operations to a private contractor, freeing NASA to pursue its research and development objectives. And the Air Force makes no secret of its desire to dissolve its partnership with the agency.
Last month, the Air Force announced the formation of a Space Command, analogous to the Strategic Air Command, to coordinate its activities in space. It also established a Space Technology Center at Kirtland Air Force Base, N.M., to oversee research in space-based weapons and surveillance." http://www.nytimes.com/1982/07/11/weekinreview/for-now-it-s-nasa-s-deck-but-pentagon-holds-the-cards.html
The intent by the Pentagon to establish its own space-based branch independent of NASA was eventually realized, as their operations of the X-37B illustrate:
“The X-37B began as a NASA project to build a small, unmanned space plane. NASA handed the project over to the Defense Advanced Research Projects Agency in 2004, but after budgetary problems the program was transferred to the U.S. Air Force Rapid Capabilities Office, which continues to manage the X-37B program. Boeing’s Phantom Works division built two of the X-37B spacecraft.” http://www.thedailybeast.com/articles/2014/04/07/will-the-pentagon-s-secret-space-plane-ever-return-to-earth.html
You’re asserting that the DOD’s control over its space-based missions that involve NASA is tantamount to control of the entire agency, which is semantic malarkey. The Pentagon carries out top-secret operations in close cooperation with the State Department—does that mean it controls the Department? Not only has the US military established its own USAF-controlled presence in space—substantially reducing the need to work directly with NASA—the Pentagon has no role or interest in the Philae lander or the recent Pluto mission or the various rover missions on Mars, which among other things were specifically tasked to look for signs of life. If you think that the Pentagon would have suddenly big-footed the Mars rover teams—comprised of hundreds of civilian researchers, scientists, and engineers—and prevented them from announcing the discovery of life—one of their publicly hoped-for goals—you’re the one who’s been reading too many Hollywood screenplays.