In the manga, she is lured into the library by an alien, and had her torso eaten by it. All is well, she's revived. It adds in details about how they can do that to the girls. Death isn't always the end.

But in the anime, which was purposely different, she seems to have taken her own life, and she isn't revived. This ends the anime on a sad note, with Yuri crying over realizing her friend is now dead.

They most likely did this so that it DOES end. If she died from an alien, then it would end on a cliffhanger of "what happens next?" With her ending her own life, it's the end of Kumi, and the end of the show. Kumi had just gone through a traumatic experience, and her whole life had been this pressure and loneliness, there's a reason why she went through this. Compared to the manga, though my memory is fuzzy, she gets through that, and grows to love her friends.

You can also talk about how all of this is a representation of puberty and adolescence, and how Kumi had to grow up much faster than everyone else, even though she didn't really want to. All this pressure is put upon her and she's only in 6th grade. She's lonely, and she's stressed.

I'm really bad at explaining things