Hi Andrew, I have no idea what a saxon genitive is, haha. But I can give you suggestions on how to write this.
First thing they did, they went to the small/little village church and prayed TO the Lord. [This word ordering is more commonly heard and indicates that the church is an integral part of the village; i.e., it belongs to the village. There is not too much difference between "small" and "little," although the word "little" carries a slightly cuter connotation - in a charming way.]
First thing they did, they went to the small/little church IN THE village and prayed TO the Lord. [This word ordering simply indicates that there is a church that happens to be located in the village.]
"First thing they did" as a standalone phrase is a bit informal. If this text is to be written in a casual context, or indicating a person's speech, it's ok. Otherwise, you may choose a more formal phrase like, "Immediately upon arrival, they visited the . . ."