My interpretation of Jon regarding the Not! Sasha situation is that, on some level, he knew the entire time something had happened, but he purposefully looked away from it because didn’t want to face the truth.
While it’s said in canon that Jon trusts Sasha more than Tim and Martin and that’s why he’s willing to give her more passes, it’s also worth noting that Jon’s bar of trust is in hell. He says that he can’t trust anyone multiple times, and the quote “I may not entirely trust my assistants but I won’t lose them,” comes from a time frame where Jon is under the impression that Sasha is alive. By his own admission he doesn’t entirely trust her, and yet he’s willing to overlook things he’d try to exorcise Tim and Martin for.
And I don’t think that’s because Jon just randomly swings between being overly trusting and overly paranoid. Rather, I think he knew something had happened when Sasha came back without the tape recorder. Because think about it: Jon’s character could be summed up by his thirst for knowledge. Yet, when Sasha tells him that information about Prentiss’s attack was lost…he just accepts it. He doesn’t question it. He doesn’t look for the lost tapes. He doesn’t even keep an eye on her.
Overall it seems like he acts really out of character, and I think that’s because he is. For the first time in the series he doesn’t WANT to see something. He doesn’t want to know if something happened to Sasha in the evidence room, because if it did, it means he might have lost one of his assistants. And it’s as Jon says himself: He won’t lose them. Even if that means turning a blind eye.
So, yeah, I think Jon’s attitude in Season 2 of “Sasha threw a knife at me today. I’m sure it’s just because she’s practicing her aim” was out of subconscious denial of the truth instead of blind trust. Especially because it would be consistent with one other knowledge Jon turns away from…which is Gerry’s page. He burns it because he cares for the people around him more than knowledge itself when push comes to shove. And unfortunately in his case that’s a great motivator of ignoring a monster.