Re-reading the story, I see a lot of evidence that Dumbledore didn’t know that Quirrell was Voldemort. For example, Chapter 62:
You are no longer taking lunches in Diagon Alley, even with Professor Quirrell to watch you. Your blood is the second requisite Voldemort needs to rise as strong as before.
He refers to the same issue when talking to Bones. It would make no sense for him to do so if he believed that Voldemort had constant access to Harry and countless opportunities to “accidentally” obtain his blood (as indeed happened with the newspaper).
Re-reading the story, I see a lot of evidence that Dumbledore didn’t know that Quirrell was Voldemort. For example, Chapter 62:
He refers to the same issue when talking to Bones. It would make no sense for him to do so if he believed that Voldemort had constant access to Harry and countless opportunities to “accidentally” obtain his blood (as indeed happened with the newspaper).