Eh...no."Thank GOD Steam exists!"
Exactly the same thing can happen with steam. A lot of indie games get rejected, actually. Of course that's also in order to keep some quality on the market, but in the end the correct quote should be
since even if steam had rejected him, he could have simply sold it from an own website."Thank GOD that computers exists, and we can basically do anything we want with them."
With America being Nintendo's most important market and children (and their parents!) making up a large chunk of their audience, they cannot make such a move. The press backlash would be incredible and not even remotely comparable with this. They could release it in Europe without any problems, though. steam has an entirely different demography to begin with, you can't compare them.
I also don't like Isaac, and think it's extremely overrated for a shitty flash game - not to mention the main dev is a retard -, but that's an entirely different matter and hasn't influenced my post.