Fair correction on the altitude (still in the lower bounds of the balloons, as I mentioned).

The SR-71 already flew in the configuration I mentioned. It's the YF-12C (a converted SR-71).

Recovering and converting another sure is more expensive than one missile, but it's a reusable platform.

A ground missile able to reach those balloons is more expensive than a modernized SR-71 sortie. High-altitude, precision missiles are also not allocated for this task. China can launch dozens of balloons for cheap, and spending one multi-million-dollar missile on each is insanity. Even the long range air-to-air ones are too expensive for that.

The SR-71 (as a new YF-12D interceptor) makes more sense. It can take multiple balloons in one flight with cheap shorter range air-to-air missiles (or maybe even cheaper weapons, for a balloon a laser would do), then go home and do that over and over again.

China can launch a lot more than a dozen balloons, perhaps thousands if convincing decoy payloads can be made. The A-12 was intended to counter high-value targets in a limited number, not low-value targets en-masse.

I can't rule out that Issacman does have this mission profile in mind, but it seems contrived. Whatever weapon the SR-71 could carry to-altitude could be be done cheaper, more numerously and probably more quickly too with F-15s. Refurbishing a fleet of SR-71s and a fleet of KC-135Qs would be a lot of work for an extremely limited capability.