First off, I think it is very well written. I like your use of description and I certainly get the feeling of the pain and horror the boy is going through.

As to where to go from here, I have a few suggestions.

Could Fr Stefan maybe escape with the boy and take him off somewhere with him?

Maybe tell part of the story from the boy's point of view.

Have Fr Stefan mid rape etc when Fr Ignacio comes back in and finds them - maybe Fr Stefan is then punished?

These are just a few ideas, but I hope they are some help to you. You have a wonderful start here, so don't give up. However, it also stands as a good short story as it is too.

Have fun
Aussiegirl