If it happens again, lets' hope the Church doesn't have another Diego de Landa on the committee.
This was a dispute, because many people in Europe couldn’t imagine that there was anything human outside of what they knew. It took orders from the Pope to make people accept this.
As for exterminating native religions, the sooner, the better. These were vicious “religions” based on fear and the maintenance of a royal house.
Only one Indian in Mexico was ever put to death by the Inquisition, because he had been educated in Spain and knew the difference between right and wrong but still practiced witchcraft. Syncretism was a big problem, but most of the people who engaged in it were too ignorant to know the difference, and hence were simply instructed and told to stop whatever it was they were doing.
On the other hand, Spaniards, particularly the clergy, were severely punished. The great majority of those punished by the Inquisition in the New World were Catholic clergy, sometimes for syncretism, but usually for things such as enslaving the Indians, stealing from them, sexual abuse of Indian women in the missions, etc.
And they were generally punished by being put to death, making it clear that the Church then knew how to react appropriately to evil behavior.