Hanako is a different case in that her
reason for attending Yamaku is, at least to some degree, psychological, which is simply not true for the other heroines. A Mary Sue character is ideal, flawless, and unrealistic. It's never too late for a character to become a Mary Sue, and losing the flawed aspects of the character somewhere down the natural progression of the story is a great way to ruin a work of fiction. Ever read a book or watch something where the main character starts out realistic and then ends up overcoming all challenges, becoming everyone's best friend, and essentially perfect? (Bleach, I'm lookin' at you!) Now, apply that to the heroines in KS.
Lily comes off as refined, but the way she's written gives off the vibe that she's repressing whatever her negative traits may be.
Emi doesn't get as much screen time, but neither Kenji, nor Shizune, nor Lily hold her in high regard for her recklessness.
Rin heavily reminds me of Osaka from Azumanga Daioh, she's the kind that's constantly lost in the clouds, usually for the worse.
Shizune is defined by her competitiveness and businesslike attitude which puts her at odds with everyone. Then there's drama courtesy of the Student Council (as with Lily).
Compare those to Hanako, who's extremely traumatized, and everyone is afraid of telling her off for anything because she would implode on the spot.
Of all the characters, Hanako's flaws are the most difficult to expose: she is characterized as extremely fragile. Hanako will remain a flat character unless her fragility (or some other flaw) is exposed and confronted. I can foresee a falling-out with Lily to that end. Of course, all the other characters can end up at the bottom of the boring character pit in as little as a paragraph.
Again, there's not much to go on from just Act I to claim any of the heroines is a Mary Sue (the bar for non-heroines is set lower), and I do trust that nothing I've written is new to the writers. Most people probably wouldn't be able to discern the quality of a character in the first place, it's not like Bella Swan (
Twilight) was a literary praiseworthy character.