Well, judging for what we have observed in game, the Thargoids seem to adapt very slowly to new events. The example of this is how long the took to adapt to our maneuvers and basic tactics (ie learning to dodge misiles, resistance, etc).
It may have happened that a "trigger" made the thargoid ships from the hive to wake out. The thargoid hive ship may have warned that it received heavy damage, so all ships and thargoid "evacuated", now knowing that they were already infected. It could also have happened that unaware thargoid ships jumped into the system later on to investigate, further spreading the disease. And, finally, maybe this "hive ship" was so incredibly vast that its lost supposed a genocide itself, forcing the Thargoids to retreat before further damage could be taken.
It i also possible that John Jameson's attack was just the first of a series of strikes. First hitting the "headquarters" of the Thargoids, then bombing the rest of the thargoid sites and ships while they were still trying to find out what had hit them.