Also for /u/oerangbandoeng and /u/Neither_Green_3337:

My interpretation of that decision -- blaming the priest is the right thing -- is that it coincides with (a) the historical backdrop of the witch trials, (b) modern-day abuses perpetrated by members of the Church, and (c) people unwilling to go against a so-called "man of God."

• The first one denotes the mass hysteria and cruelty that happened in the actual witch trials in history, all in the name of religion. The priest in 1692 (Fr. Carver) is simply a stand-in for the church's authority.
• The second one is an implication (from a few secrets) that Megan was being "disciplined" by the priest in 1972 (Rev. Carson who's also a stand-in for Carver), and a hint that she might've been abused.
• Lastly, it's the notion that there are people who will continue to blindly believe someone cloaked in that premise of being a "man of God." Carver states that "no one will believe Mary." In Carson's case, a newspaper clipping cites that several of his parisioners thought he was a good man and that accusers are simply fabricating lies.

Put all three together and the two timelines (1692 and 1972) are analogous to each other -- that people suffered at the hands of those who were supposed to be "the good people" all in the name of (or with the influence of) religion.