It was definitely a joke. As someone pointed out early in the thread, lampshading. We know Onee-san is a creepy pedo but in-universe she's the main character, not a villain... She would never do anything to hurt the Otone... But she's a sick pedo full of creepy desires, which we can see from outside of the universe.
Probably one of the most central tropes of loli stuff is that the lolis are always enthusiastic. I think there was even a study on rape in hentai manga that came up with it being rarest in a few magazines (one being 0%, an editorial decision I applaud) and number 2 or 3 was Comic Lo, which you can guess from the title is a loli manga. The suspension of disbelief is that this is all a-ok and the way that disbelief is suspended is by the trope of willing, enthusiastic lolis.
This should be made part of obligatory reading for anyone that harps about the lolicon/shotacon genre as being inherently immoral.
Welllll... I don't think that's quite the slam-dunk you think it is. The argument that the "inherently immoral" crowd makes (besides "eww") is generally one about normalization — that consistently portraying something to be true has the effect, in the public consciousness, of shifting attitudes towards accepting that it's true. It's an argument I find hard to fully refute — it's part of why stereotypes and misogynistic and biased tropes can be harmful. Portraying children as not needing to be raped for adults to have sex with them is, on this view, just a leeetle sketchy.
That said, I think the harm-by-normalization argument depends on the portrayal really being mainstream or large-scale mass media. The mere fact of being published or being available on the internet doesn't rise to that level, and we're all well aware, going in, that these are fantasies without much reference to real life.
(The only other thing I worry a little about in this sort of thing is that the "comedic onee-loli" thing kind of perpetuates some misogyny; we are supposed to think that having the quasi-predatory older character being a woman is "safer", because women can't really sexually assault people. It's like jokes about female teachers who abuse boy students. Flipping the gender would make us far more uncomfortable.)
Anyway, I really do like this series, and indeed a lot of stuff that's considered sketchy, and in no way do I want to stop anybody from enjoying any fiction. But I find it useful to maintain an awareness of what is actually being said, and a sense of ambivalence about how "harmless" anything is.