I can't speak on the relationship between the Church and the cartels specifically, but many of the wealthiest narcos are significant social benefactors in their home regions. It's a brilliant strategy - it legitimizes their organization in the eyes of the citizenry, by addressing real needs that the state has failed to fulfill, and in so doing simultaneously delegitimizes the state.
For example in Sinaloa, El Chapo's home state, he's regarded by many as a "Robin Hood" figure because he's built schools, churches, hospitals and more in impoverished mountain villages that receive little to no aid from the state. In return, he was for years able to move freely and conduct his business with impunity from Sinaloa, without having to worry about locals betraying him.
For example in Sinaloa, El Chapo's home state, he's regarded by many as a "Robin Hood" figure because he's built schools, churches, hospitals and more in impoverished mountain villages that receive little to no aid from the state. In return, he was for years able to move freely and conduct his business with impunity from Sinaloa, without having to worry about locals betraying him.