Well if you put this situation in protagonist's prospective, this is certainly a story of NTR. Actually it goes beyond that
Protagonist had affection towards his sister, but she ditched him and got marry to someone else. Although protagonist continued sexual relationship with her sister anyway and I believe she didn't mind it, at the end, the sister revealed that she is pregnant of her husband's baby and clearly refused any more of sexual relationship with her brother, showing that she clearly loves her husband and her child more than her brother, the protagonist.
This is a case of between lust and love, which is a popular theme in literature.
You see, to satisfy our sexual fantasy, lust often wins over love. It implies that all women are same when it comes to female orgasm. They are whores, sluts and bitches. Thus, female characters are often sexually dominated by sexually capable assholes and fall in love with those assholes who treat them like shits. As story progresses, female characters often abandon everything, including her boyfriend, childhood friend, brother or anyone who cared those female characters dearly.
However, in this manga, love prevails over lust. She refuses to be ruled by emotions by rejecting having further relationships with her brother. It shows she has grown into a responsible adult, mother and wife, leaving her raped and miserable memories of adolescence behind. Actually the artist hinted in the last page that even the protagonist who is in great grief would find a new love.
When you think though it, the plot is pretty deep. I reckon it is one of the most interesting plot from this artist.