If its the signatures that are the problem, why not blank them out?
Shouldn't be too difficult to semi-automate, assuming the signatures appear in a defined place (usually the end) rather than being scattered randomly throughout the documents.
Of course, the long term answer is not to scan any future documents but to require them to be created online in the first place. That would make it much easier to create a "safe to distribute" version for online download, omitting such parts as might be considered a security risk.