Indoor toilets require water on demand in every home, which is a VERY recent innovation around the world. You use the water both to flush waste but also as a barrier between the sewer pipes and the home, to prevent odors and flammable/explosive sewer gas from entering (a modern toilet is also a nontrivial industrial product--large, reliable metal and porcelain castings are relatively recent, too). Until you can use water to remove the waste, a bucket with a tight lid is the best option (aka a chamberpot) followed by an outside bucket with a door (aka an outhouse).

Also, seriously, how could the Church have possibly caused this? The majority of the world that's not Christian had and has the same waste removal strategies.