I don’t think you can get a lock on the balloon envelope.
They were having trouble with a radar lock-on before firing They just maintained visual contact. I don’t know how much of a thermal fingerprint an AIM-9X needs to find a target. Seems like ambient temps would be pretty low at that altitude. The sun could have had the balloon and payload somewhat warmer. Seems that a TV guided missile could have been used to go right through the balloon.