Never underestimate a company a large as Apple missing out on nuance in art. I've written extensively on The Binding of Isaac and it's sequel/remake Rebirth in the past. Suffice it to say, I'm a fan of the property.
Yes, it's an uncomfortable game when looked at on a literal level. It's a twisted horror version of the biblical tale of Abraham and Isaac. That's where God told a father to tie up his son and execute him on the altar to prove his faith. Right before the death blow, God stopped Abraham and said he passed the test.
The difference in Binding of Isaac is that Isaac's mother gets the first message from God, but no one intervenes on the execution. Isaac travels through layers of his basement to escape his homicidal mother who believes she is doing God's work.
So, again, I'm not surprised that the Apple Apps store rejected The Binding of Isaac: Rebirth. It's violent and disturbing. The reason for the ban is quite stupid: violence against children.
A store that has no problem selling Limbo--a game about a child escaping death from natural hazards, manmade hazards, and other children--and a whole lot of zombie games where children can easily die says a satirical game about faith with cartoon-style is unacceptable. That's where it gets just a bit too ridiculous.
YouTube channel The Know has the best breakdown of everything that's wrong with banning The Binding of Isaac: Rebirth I've seen. They unleash a righteous rage on double standards and the notion that video games can't be art.
Which, yes, this kind of hand-holding censorship justified by saying "kids browse the apps store, not the book store" is grounded in the belief that video games are just for kids. They're not. Shame on Apple for not being with the times.
The good news is that you can easily get The Binding of Isaac: Rebirth for PC and PS4. Nintendo backed off of its initial ban (based on a flat "no religion" policy, which makes a whole lot more sense than "no violence against children" policy) and the game will make its way to the New 3DS eventually.