Never really understood the Japanese mindset of getting married and having children, even if that isn't what you truly want. Traditionalism is lame, and so is the chick who got married in this one-shot.
There was this one episode on some Japanese talk show where guests from various parts of the world were shocked and perplexed to find out that the Japanese there considered looking for a lover and looking for a spouse as two separate things. They said they look for financial stability and not love when it comes to finding a spouse, while they may not ever have any intention to marry when looking for a lover.
Likewise, the Japanese on the show were incredulous that the foreigners considered their lovers to be the one they eventually would marry. When someone said they'd do whatever it takes for their partner to achieve their dreams, even if they have to financially support them during that time, one of the Japanese said something like "He's a bum! Don't marry him, kick him out!"
Probably a big factor in some people's confusion is the troubling general hentai convention of "no means yes." Pretty much every h-manga, even yuri ones, even ones featuring established couples in a relationship, feature this kind of non-consent play. I can imagine it creates a very confusing (or fucked up) idea of how seduction and sexual progression should play out in a relationship for people who can't put this stuff into context.
Anyway, that creates a very difficult situation where it's hard to tell if the author intends a particular situation to read as rape (and it's bad), rape as a sexual fetish, or non-consent play (where what's going on is ok for that couple, but in order to seem demure or whatever one partner protests). As a non-fan of any of these things I have learned to mentally block them out most of the time but it's nevertheless a minefield that exists in manga (and particularly h-manga).
It's a language and cultural lost-in-translation thing.
More about speaker concerned about self 'behaving improperly' (in the veins of "i'm going to let out an improper noise") rather than protesting the advances.of the other in a consensual scenario.
Misaki being the naïve girl living a cozy, carefree life that she is, trusted Jun a little too much ("She's Tsubasa's friend, I can trust her"), and is confused by the sudden unexpected non-consensual sexual contact. I doubt she ever thought about the possibility of getting raped ever in her life and she's now taking awhile to process the new information, being helpless in the meantime. Doesn't sound far-fetched to me.