I think you're reading a lot into the conflict between Rick and the President that isn't really there. Rick just thinks that he's a force of nature beyond normal laws, and the conflict is about whether or not this is true, but obviously it is because he's Rick. The President is unhappy about this state of affairs, but ultimately decided to let it lie; he goes back on that in this episode and ultimately lets it lie as well.

The theme of intelligence does play much more strongly with the interactions between Rick and Beth - as you say, she knows that he would lie if asked a question so she can't trust him. But I also think she just is in a bad place and went for the comfort of a guy who is simple and more importantly cares about her and thinks very positively of her and so forth. Also, I don't think the part about trust is as directly related as you think - if Beth really was a clone, then how would Jerry be able to tell? That's why I think it's more about just generically "being comforted".

"but it isn’t the status quo, Rick has just been defeated, and defeated by Jerry"

I see your point, but I think the family ultimately defaults to the Season 1 dynamic. Especially since it's not like Jerry planned this out and will think "Yeah, I beat Rick". More like, "I got lucky". Also, the weak point of Rick's nihilism is that he drinks a lot and does stupid stuff and screws up a lot, as shown in Season 1. I don't think what happened here is an especial weakness of nihilism or anything along those lines.