Idaten Gods spoilers

So the scene at the end of episode 1 comes at the end of vol 1, which is chapter 7. Episode 2 has one half of that scene, where Isli is talking about how the Idatens' help of humans, or lackthereof, is an issue of scope - at their power level and grasp of reality, no one human is important. Neither is any given amount of humans, except _all_ humans. That's why they don't meddle but fight demons instead.

This is meant to show how detached they are from individual suffering and individual wishes of salvation.

Also, in chapter 7, we see the part in episode two where the general eggs on soldiers to do horrible things _before_ the rape scene, giving it at least some immediate context.

But in episode 2, where he explains this, we see scenes of other human cruelty and suffering, and just an implication of rape that is Not Good, but at least not tasteless. The production _chose_ to keep an explicit rape scene for no reason other than adherence to the source (which includes censored full frontal female nudity). The scenes shown in episode 2 are not part of chapter 7, which causes the entire rape scene to be even more unnecessary.

AFAIK, that nun character doesn't come up again, at least for a long while (nowhere to be seen in vol 2).

tl;dr - someone read Berserk and took the wrong lesson from it.