I think that the most compelling answer to this would lie in one character's name: Abigail Williams. John recognizes from the opening act that all of this hysteria regarding witches, what happened in the forest, and the notion of spiritual damnation is a front and a complete sham. He understands that Abigail's true nature is to bump off Elizabeth and claim John for herself. John understands that Abigail's ability to manipulate the people of Salem to benefit her own agenda is what is at stake. When he refers to Abigail's reception at the hands of the townspeople as taking the word of "whores," he is deadly serious about how Abigail's personal agenda is driving the political and social agenda of Salem. In the end, the injection of personal desires being used to drive political actions ends up becoming the fundamental sin of Salem. This is something that endangers the order of Salem, as well as the political order of all democracies.
The fued between the Putnams and the Nurses over land seems to be a great originator of the evil afflicting Salem as well. The Putnams have ill will against the Nurses for not supporting their brother-in-law as the new minister as well as disputes over land... where boundaries lie.
It also seems as if the Putnams encourage the girls to cry out names of people associated with the Devil. The Putnams had sure already made their share of complaints against people known to be upstanding citizens. If you listen to Mrs. Putnam speak about Rebecca Nurse, there seems to be an apparent jealousy about the ability to have healthy children.
These pieces of information demonstrate the Putnams had purpose for revenge. Anyone associated with the Nurses (including the Proctors) incurred their wrath.
The evidence comes in many ways: First, the rampant war that the Putnams have with everyone over land which they feel they were owed. Second, he knows that the Putnams would stop at nothing to remove people out of their way to get what they feel the deserve. Second, although he tried to keep it hushed, he had sexual relations with Abigail Williams and she is vindictive and would easily put John's wife in trouble because of jealousy and due to the anger that Elizabeth caused Abigail when she fired her from their home. He also knows the secret ways of the elders, the secret cliches of the settlement, and the double standards by which everyone seemed to be living.