From the government's perspective, a capsuleer developing the planet (notice, by the way, that he said that the emplacement of facilities was automated, not the operation of them) is a wonderful thing. It's infrastructure development with no overhead for the government. Jobs will be created, etc.
Now, was the capsuleer's threat a bluff or an actual intention? I'm going to go with "bluff". After all, capsuleers up to this point have been characterized as often inhuman, impatient, selfish bastards. This fits right into that: the pilot can't actually bombard the planet without a CONCORD response, but the planetary administrator doesn't know that. He's not a pod pilot, he doesn't know the rules "we" live under.
So the capsuleer threatens, the reputation capsuleers have works for him, and he gets his way. Selfish, petty, powerful, and without ethics. That's not a new story device.