The Auror saw Quirrell fight him with amazing skill, attempt the killing curse, and turn into a snake. Harry saved him from the killing curse. Quirrell's the clear bad guy from his point of view (is that enough evidence for people to conclude that Q=V?), and only Harry's last Somnium spoils his innocence.
It will also be clear that they were lying to Bella, at least about some important things, since it was Harry's Patronus.
I'm pretty sure I'm being exceedingly careful here, but...
is that enough evidence for people to conclude that Q=V?
It's enough evidence to conclude that he's a bad guy.
Assuming I had never read Eliezer's assurances that Q=V, I would most definitely not put it past him to make his rewriting of HP not so much about the Dumbleharry vs. Voldemort war, but about the internecine fight between Quirrell/ColdHarry and Dumbledore/WarmHarry about how to confront the Voldemort threat - by finding a worthy dictator (in the original intent of the word, hopefully) or...
[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
Spoiler Warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.