The other possible explanation is that it implicates high-ranking Saudi officials, which would make it politically problematic to maintain the existing diplomatic and security relationship. For example, while under seal it can't be used to civilly sue those officials, and it permits the DoJ to avoid prosecutions it might be politically forced to pursue. Such civil and criminal suits would disrupt the existing state of affairs. By keeping the secrets you keep closed the pandora's box of political pain, even though anyone who cares already knows what's in the box.
People outside the government have read the files. As the article says, lawyers for plaintiffs in the ongoing civil suit saga have seen them, as presumably would the judge. If the documents detailed criminal activity on the part of the U.S. government we'd have heard something about it by now.