"The Pentagon is the headquarters of the United States Department of Defense, located in Arlington County, Virginia. As a symbol of the U.S. military, "the Pentagon" is often used metonymically to refer to the Department of Defense rather than the building itself."
You can find soldiers at the Tomb of the Unknown Soldier, that doesn't make the tomb a military installation. The mere presence of military personnel does not make a facility a military installation. Since the Pentagon is where the civilian leadership of the military is located, the building is arguably a civilian facility.
I am aware that JCS meets in the Pentagon, what is the point you are attempting to make? The fact is no troops are trained, quartered, & mobilized for war in the Pentagon. The Pentagon is a civilian location. In the U.S. civilians run the military (in other words the chiefs answer to their bosses, the secretaries, who answer to their boss the SecDef.)
Tora Bora is where the Taliban trained, mobilized, & quarter troops (even if they were irregulars.) This is the distinction between a military facility & a civilian facility that happens to deal with military affairs.
http://en.wikipedia.org/wiki/The_Pentagon
If you go there, you will find soldiers ready to use lethal force in order to protect portions of the building.