I liked the ending. I interpret the conversation the girls in the bookstore were having about Beniko's happy endings straining suspension of disbelief as a metacommentary on the story itself. Beniko writes stories where her characters' love overcomes all obstacles and they get a happily-ever-after always. The lovers' suicide made her feel the same as the one bookstore girl feels (that romantic happy endings are unrealistic) and consequently she was unable to finish her book. But all that was just another obstacle for her and Yuki's love to overcome, and when they get back together Beniko finishes her book and returns to success. The same is true of Yuki's dad, who has an "unrealistic" change of heart and decides to let his daughter run off and be with Beniko because she is in love and that is what would make her happy. And the girls in the bookstore kind of relate all this to the reader of the manga in an indirect way with their debate about the endings (specifically the endings) of Beniko's books.
Of course we are talking about a character's take on a fictional work within their own fictional world, though, so in a way it is kind of like the story is talking directly to any readers who might identify with Yuki. They are the Yuki reading about Yuki reading about her Yuki. If the reader sees it as just an unrealistic ending, however, maybe the reader is more like the bookstore girl, and really also like the suicidal lovers whose love did not manage to overcome all obstacles.
Or maybe I'm dumb. Without the meta part, it does seem on the face of it like a bit of a rushed ending. But secretly I'd rather be a Yuki.
I think the conversation is important as a plot device to get the father thinking about his daughter's happiness. The women are discussing not only the book's endings, but they're discussing how there is no happy ending for women that fall in love with women. How the harsh reality of the era means that happy endings are just a fantasy. It basically slaps him in the face with "Your daughter is miserable and you're hurting her." That changes his perspective when he sees her again, so after she breaks down he decides to read the book and understand her feelings, rather than just push his will onto her. And once he understands how she feels, he can't bring himself to force her into the marriage. I actually think it's pretty beautiful in that respect. He takes a stand against the expectations of society to protect his daughter's happiness. And it's pretty clear from what we see of his personality that that is contrary to his personality, which makes it a real act of love.
I can see how it could be taken as meta commentary, but I really think it's mostly there to push the story in the right direction.