Let's face it: very few Yuri manga/ DJ are realistic. Come on, would any sane couple do this at school, right by the staircase? Wait actually don't answer that, we've got a few bad asses here The fact of the matter is that the culture has somewhat been fabricated through this kind of media, which is, I think, where the "No means yes" notion came from. It's been over used so much to the point where when I see a Dj where "Yes" is written, I'm taken aback. Which is why I like Tima's work: no dialogue is written during the sex scenes, apeasing both the "Yes" and "No" factions.
At least in the high school I went to, there were couples who would get a little too touchy-feely on school grounds -- it's not that uncommon. That aside, this is a common setting for doujins (school/classrooms are unsurprisingly popular) and it's a fantasy.
the culture has somewhat been fabricated through this kind of media, which is, I think, where the "No means yes" notion came from.
If you're implying that the idea of "no means yes" in Japanese culture is something that came from doujins, you're severely, severely misinformed. It's a very prevalent element of Japanese culture that you'll see in other areas (for example, in Japanese culture many don't flat out say "no" to an offer, but instead will indirectly imply a no. Another example is when being offered something; they refuse the first two offers -- if a third offer is made, then you can accept). In terms of sex, if you've ever heard the phrase 「厭よ厭よも好きのうち。」 (or roughly translated, "'No, no' can also mean yes") it can help to understand some. While a cliched and controversial phrase, it is a part of understanding the role that phrases like ｛いや」 and 「だめ」 play in doujins, and why you hear it so often; innocence is a huge part of Japanese feminine idealism. If anyone's ever heard of idol scandals where the idol in question was accused of having a boyfriend or sleeping around, and seen the huge backlash that she gets for that (oftentimes having to quit her career), then that may provide help as well. A striking example is Minegishi MInami (http://en.wikipedia.org/wiki/Minami_Minegishi), and perhaps another high profile case is Hirano Aya's. Innocence/purity is a major part of what makes of the "ideal" woman in Japanese culture and leads women to display shame/reluctance in regards to sex so as to maintain that image of "purity". The moral implications of that notwithstanding, it does make sense why you see it so much in doujins, and why it isn't really "rapey" in keeping with the culture the media is from.
Point is, the "no means yes" thing isn't something fabricated through media. It is a part of Japanese culture and language outside of the bedroom. It just happens to also play a part inside of it, too.
I'll repeat: Discussing problematic elements is not a judgment call on the media itself nor the people who consume it. It's about awareness and, although less so with this particular work as we can hardly influence the Japanese scene, hopefully about improving the general quality of media as a whole.
I can almost guarantee you no Japanese doujin artist/author is going to read the comments section of this site and decide to radically change Japanese culture. I agree that the discussion of "problematic" elements doesn't mean judgement, but at the same time, context is key. You have to remember that Japanese doujins aren't intended primarily for Western consumption, and that they're not targetting a Western audience. Why would they completely change the cultural context of their work for them, and why would a separate audience debase it? I'm not saying you can't find fault or disagreement with it, but at the same time, there's no need to imply that the removal of cultural context in Japanese works intended for Japanese audiences will "improve the general quality of media as a whole." Not only is that pretty insulting, it's narrow-minded. Having something agree with your moral compass =/= improving the entirety of a media.