Based on what you said the W-2 shows, (If the 941s are the same) ALL of the SS has been paid.

1/2 by the church and 1/2 withheld from the pastor. I am not sure you need a credit for 1/2, or that you just don' need to report any for SE tax as it has been paid. 

Again, Not sure any of us really know what the church did, and that you would need to know before proceeding.