Thank you, fellow Patton Oswalt fan.

I know “The Binding of Isaac” is an actual Judeo-Christian term, but these days it makes you read something of that name and expect an appearance from Monstro and Larry Jr.

…O-kay. While I am happy that you didn’t linger on the actual abuse (seems more like an execution to me), and actually gave a reason behind it, it still leaves a bad taste in my mouth. Amusingly though, it’s because of the use of “Christianity” in this story.
 
Now, let me elaborate on why I put it in parentheses: What you are presenting here as “Christianity” is the pop-culture, theme-park version, or as I call it, the Ned Flanders model. You mention the whole 700-club thing, going to church regularly and attending church bake sales and stuff, as well as the whole idea of the rapture. The thing is, while these are parts of certain sectors of Christianity, they do not define it.
 
For example, and this is just an example mind you: The idea of the rapture is a predominantly American Evangelical idea, one based on rather loose interpretations of certain passages in the New Testament that isn’t accepted at all by the large majority of the Christian denominations. The fact that you use Pat Robertson as an example of a “righteous Christian dude” seems also somewhat of a lazy shortcut to identify this character as “Christian”.
 
However, just because I have these critiques of the story, doesn’t mean that it’s without merit. I highly respect the fact that you made sure to show that the human in this story is an actually committed Christian, first adopting Ishmael due to what he feels is the right thing to do by God’s law, then killing Ishmael because he is true to his faith. The fact that it turns out that by killing Ishmael relatively quickly, he spared Ishmael from dying in the Apocalypse, is a rather nice touch. I just wish that we could have seen the man’s soul reunite with Ishmael’s, if nothing else as a reward for following God’s command.
 
Oh, and one last thing: Naming the pony Ishmael? Brilliant sir, brilliant.