Freemasons had to be eliminated because they actually posed the biggest threat to the religious world by allowing people to be free thinkers. This is not a good thing for the business of religion and the order had to make sure that freemasons did not gain enough power to continue to be a danger to the world. The best way to eliminate this problem was to come to an agreement with them and allow them to live without restraint as long as they agreed to stop propagating their rebellious message to the world.
There is no way to stop human beings from having rebellious thoughts, but the order needs to keep this kind of revolution against religion from growing too big. The more people who are able to remove their blindfolds from religious beliefs, the more control that the corporations and governments will lose. Anarchy would be a very common occurrence if religion is no longer feared.