I don't know which weapon would be used. A laser or a machine gun can take out a balloon if you're close enough. Even if missiles are used, closer range air-to-air are cheaper.
Also, approaching the balloon in stealth with a plane that has its own radar system is considerably less paraphernalia than ships chasing balloons.
I could be wrong about how the SR-71 will be used, but I'm very sure using expensive missiles designed for much more advanced threats to take out balloons is insanity.
You can't gun kill a balloon floating at 60k feet. That's not going to work. It has to be with an active or semi-active radar homing missile.
The loadout will be like an F-15 with just one or two AIM-7 type missiles of appropriate generation and maybe the center tank. You configure and fly the plane to the altitude as usual, then when instructed, push the throttle all the way forward, do a shallow dive, then pull up to the precise absurd angle as you were briefed and keep it there. The number on the right go crazy and the number on the left goes down slightly less faster. At some point, you will see an angled rectangle with a dot in the center, itself in the center of a large circle on the HUD, and it says SHOOT, so you pull the trigger. You here the thunk of missile leaving, then nothing happens for 30 seconds, and the radio says target radar contact lost as expected, you do a 180 roll into a shallow dive and go home.
I mean, that's how I as an armchair flightsim pilot think it'll go, but I'm sure this wouldn't be way off. Attempting the same with a gun installed on a Blackbird? That's just waste of everything from time of everyone involved to your own life.
You seem to be confused about basic aerodynamics. At those altitudes, attempting to shoot a balloon with a machine gun would be insanity. The high wing loading limits maneuverability so severely that the shooting platform would risk running into target debris.
As of today it's not possible to mount a laser on a tactical aircraft (or SR-71) capable of destroying a balloon. There isn't enough space or power available. Perhaps that will change soon but for now it remains science fiction.