I never said that a genderswapped version of KS would be the same experience. Indeed, it would be bizarre if it was, and I doubt anyone would expect it to be. The point of a genderswap is that its interesting to see the characters you are familiar with through the new lens of the opposite gender. That said, your example of what reaction the genderswapped people would incite in people. Well, its the job of a good writer to draw out whatever emotion is appropriate, so such a thing would have more to do with the quality of writing and narrative.
That said, why would it not make sense to swap the characters genders? Most all the characters have personalities that are easily transferred to a male version. If you are going through the trouble of basing the story on KS, why make entirely new people, and if you are making entirely new people, why bother making it based on KS? Especially seeing as there aren't any male characters to use, except for Kenji. The rest of Hisao's class being made up of cameos and other people with no personality or identity.
That said, Hanako is kind of the unlucky one in the genderswapping matter. This is because, unlike the other characters, she falls very much into the female stereotype of the shy quiet weak girl. Since "real men" aren't allowed to show emotion or be overtly weak, Hanako would have to be a fairly girly boy in the genderswap or risk just looking pitiful. The stereotype is completely ridiculous, and a good enough writer can still turn it around and make a male Hanako sympathetic, but its what culture has saddled males with. The other characters, however, have personalities that are pretty easily transferred to a male version because they don't really fall into gender specific stereotypes. Shizune, for example, is interesting because her scenes are like a fast tango because she has a strong, aggressive, competitive, hasty, and playful personality. If the male version could still give the same feel in his scenes, there isn't any reason why it couldn't be as enjoyable. The other characters are about the same. Misha would still be a loud and good natured person, Lilly would still be a refined gentleman/woman, Rin would still be a cloudcookolander with a penchant for non-sequetors, and Emi would still be an energetic and excitable sportsman with an absentminded streak. Whats really interesting about KS girls is that they (with the exception of hanako) are not exceptionally "girly". Thats not to say they don't act like girls, but they aren't girl stereotypes. Thats also why, with a good writer, they would still be fun to read about as boys.
Light and Dark
Good and Evil
Right and Wrong
taken from afar they blend together
and the world appears
all in shades of grey