[quote=@KoL]
<Snipped quote by Flamelord>

When did Chiyo broke her disguise? The only one who knows about her is dead.
[/quote]

Process of elimination, primarily. 

1. It wasn't a primordial. If it was, she would have been a lot more murderized, and everyone would have sensed it. Thus, it had to have been a magical girl
2. Rose, Izumi, and Elise were all together, so they have alibis. 
3. Nanako doesn't use a stabbing weapon, so it couldn't have been her. As well, she and Miyako were together for part of the night and Miyako  delivered her home, so she has part of an alibi.
4. Akame doesn't have a motive to kill Emiri.
5. Miyako doesn't have the motive. 
6. If there were another magical girl in the city, she would have been found earlier. And the way she was killed suggests the element of surprise, which an unknown girl wouldn't have.

That leaves the logical conclusion as Chiyo, the girl none of us known anything about and the one Akame already suspects of being up to something fishy.

Which doesn't change the fact that I will not be crying over this, because I'm emotionally indifferent to it from an out of character perspective.