As soon as you wake up, run to the south end of the church. You will see two sheds, run to the farthest shed from you. Enter it. After a minute or two, guards will come but will not attack you. After some seconds they will go back. In this process, open the door and kill a or two guards then quickly run back into the shed and close the door. Guards will come again but will not enter the room. They will go back again. Again open the door and BANG! BANG! Again go back into the shed for protection.
NOTE: Keep checking the maps for incoming guards. If guards are coming don't go outside. Keep doing this until all the guards are dead who are coming to you. After that, come outside and kill other witnesses who are in the mission.