The tendency is that siblings who grow up together generally aren't attracted to one another (the hypothesized Westermarck effect). The social extension of that is siblings who do engage in romantic or sexual activities with one another are assumed not to be socially well-adjusted people (i.e. something's not quite right with them). Unfortunately, most people who hear that two siblings are dating aren't going to have the patience to listen to their backstory but will instead jump straight to "what's wrong with them." That's the social pressure against sibling incest, and it's not insignificant.
I have to admit to this bias myself. I think in the case of this manga I would understand, but these sisters would definitely have my sympathy if they tried to move forward with a romantic relationship.
I think the older sister at the end is coming to grips with the probability that if she started dating the younger sister, the friends and family in their orbit (and society at large) would not be supportive, to say the least. I don't think she's wrong, even if it's unfair in this case.