There’s a lot I forgot about the source material

You and me both. Each week I have like three lightbulbs go off as it jogs my memory. For me this week it was also that the main focus is Hibiki. Additionally, I had forgotten the story point around his new gift of learning to speak Common and the issues that causes. However, seeing a character bleed from just about every orifice after simply learning a language did a good job of jogging my memory on that one.

they’re clearly at odds, and vocal about it, but can’t really do anything against each other easily

This is my take as well. When I had read the WN ages ago, the story wasn’t complete, so I don’t know what the end of the story looks like and if there is some future confrontation with the Goddess to come. However, my impression here is that Makoto can comprehend that he isn’t able to take on the Goddess yet. He even says that she would have killed him if her rules didn’t constrain her in some way. I don’t think we will get it this season, maybe a future hypothetical season 3, but I do wish that we could see more of what has been happening behind the scenes among the deities.