The exact hand mutilation and the cultural reasoning behind it (and Emilio's misunderstanding of it) is the one thing I remember really liking about the book, which is otherwise, as you said, full of characters making so many mind-boggling assumptions.

I totally would be behind the sheer whump of "character gets blamed for their own gang rape and mutilation" in an idfic, but when you combine it with some ostensibly serious (if, like you said, weirdly disconnected from actual religious thought) theology, it loses the iddy suspension of disbelief and just becomes ... weird. Which, for all its faults, isn't a trap A Little Life falls into.