Sorry, but the a priori assumption that Hermione is the heroine is why this line of reasoning is flawed from the start. (That and the fact that all of the friendship moments you cite as "evidence" for the ship are just that--friendship moments, nothing to do with romance or love.)
A hero is a protagonist who is also the "savior" of the piece. A heroine is simply a female hero. The hero--male or female--saves the day or the plot revolves around him/her, and the hero's actions or predicament initiate the crucial elements of the plot and solve the plot problems in the end (unless it is a tragedy, in which the hero/protagonist's LACK of a solution is the focus). Because most literary works have one protagonist most do not actually HAVE both a hero and a heroine.
That is true of the HP books as well. Harry is the hero and there is no heroine. We see 99% of the story from Harry's PoV, not Hermione's; we are introduced to Harry's family life at the start of the series (and every book), but we never see Hermione's, and JKR has even said that she's NEVER going to show much of the Grangers--or even reveal their names--because they're just not important. (We see a VERY detailed account, through Harry's eyes, of the family life of his other best friend, Ron.) It is Harry's fate that is at the center of the plot for the entire series and it is Harry who does battle at the climax of each book.
She spends much of CoS in the hospital wing due to fur on her face or being Petrified, and during most of PoA he doesn't see her because she's constantly studying for her extra classes. In GoF he only seems to spend time with her when he needs to prepare for a task, and when he and Ron aren't speaking he's extremely uncomfortable being with her. In OotP he's also not usually alone with her. (They go into the forest with each other but are with, successively, Hagrid, Ron and Umbridge.)
The things that Hermione does during the course of the series are things that a hero(ine) never does. A hero(ine) would not have been absent at the end of the first book when Harry confronts Quirrell/Voldemort; if this were truly her role she would not have been sidelined at the end of CoS and she wouldn't have been cowering in Hagrid's cabin while Harry was conjuring the Patronus to save Sirius and his other self by the lake. (I think that much of the deification of Hermione could possibly be laid at the feet of the filmmakers, who--extremely inappropriately--had Hermione at Harry's side when he conjured the Patronus. That was meant to be a private moment, not shared with anyone at all.) Hermione wouldn't have been absent from the graveyard at Little Hangleton if she were the hero(ine). She wouldn't have been absent, either, from the Death Chamber in the DoM when Harry saw Sirius killed and she wouldn't have missed Harry being attacked by Voldemort in the atrium of the Ministry. She would have been there for every conversation between him and Dumbledore as well, but she was not. She didn't even get to go to Grimmauld Place until the day after Arthur was bitten. That was chiefly a Weasley thing but Harry was involved--and Hermione was not, even though Ginny could have just gone to the girls' dormitories and fetched her. If Hermione is the heroine, why didn't JKR have this happen?
Hermione is sidelined during all of Harry's most important moments in life. She is not the be-all end-all of his existence. Simply being the most prominent female character does not make her the HEROINE. There IS no heroine, and no matter who ends up being with Harry romantically, she will not be the heroine either! She and Ron are equally his best friends, and both provide him with unique gifts that will help him to do what he needs to do eventually. But I doubt that they will even be in earshot when it happens. You've made the assertion both that Hermione is the heroine and NOT a sidekick, but the above shows that this is definitely not true. She is a sidekick, as is Ron. Harry is the hero and no one else. It is simply not possible to twist the books around and make her the heroine; it's not what's happening in the HP books and it's not even how heroines are defined in literature in general. The shoe simply does not fit.
Hermione is not the heroine
A hero is a protagonist who is also the "savior" of the piece. A heroine is simply a female hero. The hero--male or female--saves the day or the plot revolves around him/her, and the hero's actions or predicament initiate the crucial elements of the plot and solve the plot problems in the end (unless it is a tragedy, in which the hero/protagonist's LACK of a solution is the focus). Because most literary works have one protagonist most do not actually HAVE both a hero and a heroine.
That is true of the HP books as well. Harry is the hero and there is no heroine. We see 99% of the story from Harry's PoV, not Hermione's; we are introduced to Harry's family life at the start of the series (and every book), but we never see Hermione's, and JKR has even said that she's NEVER going to show much of the Grangers--or even reveal their names--because they're just not important. (We see a VERY detailed account, through Harry's eyes, of the family life of his other best friend, Ron.) It is Harry's fate that is at the center of the plot for the entire series and it is Harry who does battle at the climax of each book.
She spends much of CoS in the hospital wing due to fur on her face or being Petrified, and during most of PoA he doesn't see her because she's constantly studying for her extra classes. In GoF he only seems to spend time with her when he needs to prepare for a task, and when he and Ron aren't speaking he's extremely uncomfortable being with her. In OotP he's also not usually alone with her. (They go into the forest with each other but are with, successively, Hagrid, Ron and Umbridge.)
The things that Hermione does during the course of the series are things that a hero(ine) never does. A hero(ine) would not have been absent at the end of the first book when Harry confronts Quirrell/Voldemort; if this were truly her role she would not have been sidelined at the end of CoS and she wouldn't have been cowering in Hagrid's cabin while Harry was conjuring the Patronus to save Sirius and his other self by the lake. (I think that much of the deification of Hermione could possibly be laid at the feet of the filmmakers, who--extremely inappropriately--had Hermione at Harry's side when he conjured the Patronus. That was meant to be a private moment, not shared with anyone at all.) Hermione wouldn't have been absent from the graveyard at Little Hangleton if she were the hero(ine). She wouldn't have been absent, either, from the Death Chamber in the DoM when Harry saw Sirius killed and she wouldn't have missed Harry being attacked by Voldemort in the atrium of the Ministry. She would have been there for every conversation between him and Dumbledore as well, but she was not. She didn't even get to go to Grimmauld Place until the day after Arthur was bitten. That was chiefly a Weasley thing but Harry was involved--and Hermione was not, even though Ginny could have just gone to the girls' dormitories and fetched her. If Hermione is the heroine, why didn't JKR have this happen?
Hermione is sidelined during all of Harry's most important moments in life. She is not the be-all end-all of his existence. Simply being the most prominent female character does not make her the HEROINE. There IS no heroine, and no matter who ends up being with Harry romantically, she will not be the heroine either! She and Ron are equally his best friends, and both provide him with unique gifts that will help him to do what he needs to do eventually. But I doubt that they will even be in earshot when it happens. You've made the assertion both that Hermione is the heroine and NOT a sidekick, but the above shows that this is definitely not true. She is a sidekick, as is Ron. Harry is the hero and no one else. It is simply not possible to twist the books around and make her the heroine; it's not what's happening in the HP books and it's not even how heroines are defined in literature in general. The shoe simply does not fit.