wait, Quirrel killed Rita?

Squished her like a bug.

See Chapter 26:

Nestled up against the wall, where Professor Quirrell had stumbled, glistened the crushed remains of a beautiful blue beetle.

(The stumbling happened earlier in the same chapter, Quirrell covered it though, feigning dizziness.)

There's a lot of stuff in the fic that's explained only indirectly, leaving the reader to infer the truth - the Pioneer Plaque horcrux; Malfoy's belief that Harry is Voldemort; that Dumbledore is partially responsible for the potion that cleared up Petunia's appearance; the solution to Rita Skeeter's mistaken evidence (though that was made explicit recently); Skeeter's death; the self-serving nature of Quirrell's "strengthening" of Harry (learning to lose, inability to testify under veritaserum, rescuing a former minion, etc); the list goes on...