I still don't understand why people make that complaint about that episode. The lesson was that there's some shit in the world you can't explain. How does that relate to God?

This was ever an issue? I actually had to sit here and think about what episode that was. I always just took it as, "lul, pink pone is derp. Bothers purple science pone," which, to be fair, is probably the extent of what the intended audience would get out of it.

You could extend it beyond that into the realm of faith versus science, but that's the same as some people extending Frozen into a discussion of repressed sexual orientation an empowerment through embracing that identity. It's not totally out in the blue, but you're definitely reading into it far more than what I imagine the creators were actually conveying.