Kris isn't the only one Ralsei is putting their faith into
In chapter 5, we learned that Ralsei knows about Kris's fountain-making habits:
(Skipping ahead a bit)
Basically, Ralsei trusts that Kris's actions are well-intentioned and will lead to a good outcome, even if they seem rather objectionable at a first glance. Which is actually an outlook on Kris's actions I pretty much share with Ralsei, though for Ralsei there is obvioulsy a lot more at stake than for me, so putting their trust in Kris probably takes a lot of courage.
However, I don't think Kris is the only one Ralsei extends that trust to.
Chapter 3, telling Ralsei that you're going to the festival with Noelle on a weird route:
Chapter 5, interacting with the school doors on a weird route:
And of course, chapter 4, telling Ralsei that it's okay not to smile on a weird route:
If you're on a weird route, Ralsei knows about it. They seem to think the weird route might lead to breaking the prophecy, but are scared that the weird route will lead to an even worse outcome. Despite this, they repeatedly make the choice not to confront us about the weird route, and when they do, they quickly take their words back.
It seems to me that Ralsei extends the same trust to us that they do to Kris. Even if our actions seem cruel, Ralsei believes that we are well-intentioned, and that our choices may lead to the best outcome - though Ralsei is notably a lot more conflicted about us doing the weird route than about Kris opening fountains, so they seem to still trust Kris more than us.
However, I think there is a pretty logical reason Ralsei puts their trust in us:
Ralsei is aware of our SAVE power. I believe Ralsei's perspective on us during a weird route is very much shaped by this knowledge.
In essence I believe that Ralsei believes that we are doing the weird route in an attempt to find a better ending. If the ending of the weird route is actually a good one, we will keep it, but if it's horrible, we will just reset and keep looking for another way to break the prophecy.
That is also why I believe Ralsei is so fixated on giving "Kris" choices: If there is some super obscure string of choices that somehow leads to a good ending, then Kris, Susie or Ralsei would have basically no chance to find that path on their own. But with a time god in charge of making choices, we are actually able to theoretically explore every possible outcome of every possible permutation of choices. Therefore, we would be the only one that would be capable of finding this "happy ending" in this scenario.
That, I believe, is the underlying reason for Ralsei always wanting to give "Kris" choices, panicking when Susie takes choices from "Kris", as well as their enabling of the weird route.
Because, well, what if the only path to a happy ending laid on the path where Kris and Ralsei explored the upper path of Cyber City without Susie?