The usage of God in the script is nobody's "fault". It was a creative choice. The part really wasn't even needed. It helped tie the story together and offered a bit of humor.
My years of private school education resulted in many theology classes. Technically, the God of the Bible has no sex or race. Don't want to get off on a tangent, but Jesus (God as man) was Jewish. God existed before Jews or people for that matter. And why can't a black person be Jewish in the first place? Sammy Davis Jr converted to Judaism.
Many people make the assumption that God is male because the terms He and His used in reference to Him. These pronouns are used in a similar way that the term "man" can mean both men and women (as in, "…all men are created equal" in the US Constitution).
There is also the analogy of God as the Father. That simply means "He" is the first in command. It is not a gender assignment, just a way that we can understand His relationship with us. God creates; he does not need to procreate.
That being said, having God portrayed as man or woman is grossly inaccurate, but what can you do? Make God a Muppet? I'm sure there would be objections to that too. Should they leave God out of the story? It’s nice to have a little spirituality in prime time television every now and then.
That part of the film has been greatly exaggerated anyway. Her performance was very restrained. I liken Whoopi's attitude in the role to God giving us free will. It's implied that God doesn't have to meddle in every affair. That He works in "mysterious ways" and that Kermit could figure it out on his own.
There isn't anything upsetting about the film. Pepe’s part contains some sexual undertones, but much less than any sitcom today. That’s nothing really new anyway. We all know he's an edgy little prawn and we love him for it.
Anyway, that concludes this term paper of a post on Biblical theology. LOL! Next up - can God build a rock so big He can't move it? LOL! (Just kidding. It's an invalid question if you think about it.)