Because “our investigation did not successfully produce sufficient evidence to demonstrate criminal intent to violate this specific provision in court” isn’t at all the same as “she didn’t do anything wrong.”
She did lots of things wrong. She lied repeatedly to the entire country. She blatantly violated State Department policy regarding how classified information should be handled. Since this isn’t a court of law, we can acknowledge that she almost certainly did this to circumvent FOIA, as Comey acknowledged any reasonable person might infer. Although the law contains a gross negligence clause, it hadn’t been used in ninety years — so Comey notes that the FBI’s decision not to recommend indictment has less to do with whether or not she was grossly negligent (although he repeatedly describes her behavior as “extremely careless”) than it does the fact “no reasonable prosecutor” would choose to try to prosecute the first case relying on that clause in ninety years.
She put herself in a situation where the only way there’s a reasonable doubt that she didn’t intentionally break the law is if we accept that she may have been incredibly incompetent — as in, not sophisticated enough to understand some of the simplest, most basic elements of information security. The FBI concluded that the latter was reasonably possible — so intent couldn’t be proven. In the same way that in the section of the transcript you highlighted, Comey doesn’t say “Sure, any reasonable person could have missed the marking.” He says, “I wouldn’t have believed it before, but I guess it’s possible — possible — that a reasonable person could not understand what the marking meant.”
Does this mean that based on his knowledge of the case, he, personally, thinks that she didn’t know a classified marking when she saw one? No. It doesn’t even mean that he finds that particularly plausible. What it means is, if the FBI had recommended prosecution, the defense could be expected to make the argument that there’s reasonable doubt about her culpability.
I’m no fan of Clinton’s, but again, as a reasonable person, I feel pretty safe inferring that she’s probably not particularly unsophisticated or incompetent.
I would not describe these conclusions as being “cleared of wrongdoing” — even if the FBI didn’t recommend criminal prosecution.