It seems that the trials tore the church apart. There were many who wanted to rebel. We know this because in Act IV, Parris is feeling the impact as the minister of the society's rebellion. The preceding night, he found a dagger that had fallen from atop his door. Here is another comment that bears weight into how the trials are affecting the town:
Parris: I tell you what is said here, sir. Andover have thrown out the court, they say, and will have no part in witchcraft. There be a faction here, feeding on that news, and I tell you true, sir, I fear there will be riot here.
A more literal application regarding HOW the trials affected the church has to do with the new responsibility that has been heaped on people who are not yet dead or in jail. These people have to take care of extra children, extra crops and extra livestock. Some of it is just going uncared for:
Hale: Excellency, there are orphans wandering from house to house; abandoned cattle bellow on the highroads, the stink of rotting crops hangs everywhere.
Obviously, this is a townspeople, a church body severely inflicted by this great evil going on.