Nintendo allows games like Senran Kagura to be published on the 3DS, even outside of Japan, so while I'd be happy to be proven wrong, I really doubt that they had any kind of moral dilemma about The Binding of Isaac.
I think you guys are forgetting that Isaac was a Flash game. Porting it to any mobile platform would have required a C or C++ rewrite... which, hey, what do you know, was just released as The Binding of Isaac: Rebirth...
https://twitter.com/tyronerodriguez/status/53190754526770380...
Either Nintendo have lowered their standards or the increased popularity of the game makes the potential backlash a worthwhile risk.