Personally, the scene in Made in Abyss didn't even register for me.
Fist, It was clearly a joke, not fanservice. The joke is how ridiculous extreme is the punishment. They are little kids in school, but it's even harsher than what we imagine they do in the Navy Seals! The joke even had setup (that's why they did the offhand comment in the previous episode, now we see it was for real).
The characters are not attractive, in fact, apart from being featureless little kids they actually are barely similar to humans, so it would be hard to classify the scene as titillating. Hell, I think she appeared more deformed than usual in that scene.
The contrast on the vague S&Mish nature of the punishment and the reality of being little almost asexual chibi characters makes it inappropriate in a way that actually makes the joke funnier.
And at the end of the day, it was a fast 1-second cut in a montage scene.
On the other hand, dragging the show through the mud for nothing may turn people off of ever trying to experience it in the first place.
There is nothing objectionable about this unless you're concerned about child cruelty/abuse to begin with (which may be a perfectly valid reason to skip the series entirely, even before episode 2). The equivalent of a genderless blob with a head is shown, focus on her face, situation and background. It's a brief moment in a montage of life at the orphanage, mentioned prior by a character, not thrown in for a cheap loli kick. Nothing sexual or 'fan service' about it. I honestly think that only someone familiar with anime 'loli culture' could even see it that way.
I'm a little surprised to see these kinds of comments, but I suppose I shouldn't be. We all gave different lenses through which we view the world and these clearly colour our interpretations. To me, these comments feel optimistic and maybe even naive (no offence intended, I'd rather live in a less unpleasant world, but here we are).
My initial reaction to the show was not just tied to this scene (although it's certainly the worst offender) but also the repeated mention of Reg's penis. Why does the story even contain these elements or moments? Are they plot relevant? Can't Riko be punished in one of a million ways that don't involve nudity? I felt like (and this is with no prior knowledge of the source material) that the only reason for the content to exist in the way that it was to please the particular proclivities of the original creator.
Just, for a moment, consider how a live-action version of this same scenario would be received. It's wouldn't go down well, right? If that's the case, then why are we hand-waving it away in the anime? I'm sure Turin will argue that the character designs are of such a simple nature that they couldn't possibly be anyone's fetish material but again I'm going to have to disagree and say that at the very least there are plenty of people who clearly find them attractive. I don't really want to go much further down this line of the argument because it's quite subjective, but I think it's fair to say that different people are 'into' different kinds of character design.
Secondly, I don't think we can cleanly divorce anime (and manga) from their original creators and the industry as whole. There are numerous artists, animators and directors who are clearly into material that depicts underage characters. It's a seam that has run throughout these fields for sometime. Knowing this to be the case, I can't help but be
extremely sceptical whenever such material appears in an anime. I also felt the need to pull all the way back to the source material to check how it portrayed there (obviously the manga and the anime can be separated to a certain degree, but I think its telling what the director of the series chooses to include in their adaptation). Unsurprisingly, the scene is even worse in the original manga, so I guess I should be glad that they toned it down somewhat. Unfortunately, it seems that from both the actual content in the manga, and the manga author's Pixiv page, that he is very much into depictions of underage characters. Now, it may be possible to separate his tastes from the work he created, and the anime it inspired, but its
very hard for me to do that when we have scenes featuring naked underage characters.
Also, the scene was between 3 and 4 seconds long.
I guess this really boils down to how sceptical you are about the media you consume and most of the time I don't see any reason to give an anime the benefit of the doubt.