In the video (or one of the videos) it looks like the missile hit the base of the balloon, which did pop the balloon but also separated the payload from the balloon without destroying the payload.

Considering that they waited until the balloon was over shallow water it seems like a deliberate, 'surgical' move to seize the payload with minimum damage.

For public consumption this also provided a clean and decisive shoot rather than looking rather ridiculous by shooting rounds at it without necessarily any immediate effects. So a good ending for the President's image.

The fact that they it let cross the country first suggests that it wasn't deemed a threat, though.