Stinger's warning encapsulates the Cold War backdrop of Top Gun perfectly. Cougar and Maverick are definitely in hot water during this scene, but Stinger knows better than to let them fire the first shot of what certainly would have turned into the most destructive war ever.
VIPER: Although we are not at war, we must always act as though we are.
Viper says it best. Even when there is no actual war, the military has to pretend they are in order to stay sharp. In some ways, the subtext of Viper's comment is this: war is a permanent state of affairs.
ICEMAN: Maverick, it's not your flying, it's your attitude. The enemy's dangerous, but right now you're worse than the enemy. You're dangerous and foolish. You may not like the guys flying with you, they may not like you, but whose side are you on?
The real war isn't with the enemy. Maverick is, essentially, waging war on his fellow pilots (and himself), if only because he's endangering them more than the enemy is, all because of his attitude.
VIPER: In my squadron in Vietnam, we lost eight of 18 aircraft. Ten men. First one dies, you die too. But there will be others. You can count on it. You gotta let him go. You gotta let him go.
Viper describes the reality of being a fighter pilot, and the realities of war. He not only gives Maverick (and us) a history lesson about high death rates in Vietnam, but also points out that jets are almost as dangerous in peacetime as in war.
VIPER: We were in the worst dogfight I ever dreamed of. Bogies like fireflies all over the sky. His F-4 was hit, he was wounded, but he could've made it back. He stayed in it, saved three planes before he bought it… Now that's not something the State Department tells dependents when the battle occurred over the wrong line on some map.
Viper again describes the realities of war with perfect precision. He tells Maverick about his father's heroic, wartime death, and also alludes to the politics of war. Wars are fought over "lines" on maps, and Maverick has grown up believing a lie because of the contours of some dumb boundary.
STINGER: There are MiGs in the area. Tensions are high. If you witness a hostile act you are to return fire.
Stinger finally gives the boys permission to fire because he knows it's his guys or the enemy's guys. Nevertheless, he doesn't exactly give the guys a blank check. They still have to witness a "hostile act," which soon happens as Hollywood is shot down.