Well, so it's a good thing the Elders got what they wanted. Otherwise who knows what kind of pointless, destructive quagmire might have ensued?
The hostility towards Jonsu was quite unrelated to question of future crusades, and more based on her personal qualities. The fact that it allowed Medugnatos to call the crusade for Terran was an unintended consequence; indeed there was not even a hint at the possible need for a future crusade when all this took place. Had Rabisu "groomed" any other priest no one would have protested, and we would have had another anti-crusade Light of the Maddening.