Without stepping too far outside my area of expertise, and having never been a consular officer or worked in law enforcement directly, let me just say that the case you presented is essentially a case of civil liberties, if I'm not mistaken. It's a case of somebody trying to come across for a lawful and just purpose, but being denied on grounds that are maybe a little fuzzy.
My first recommendation has to do with creating evaluation and measures that could prevent some of this, looking at certain policies, and even going past the policies and looking at certain initiatives that are being put together, such as biometrics or different types of biometric protocols being put in place at your visa pre-screening processes, and judging them on five different levels. Those five levels are to look at the history, see if there's any precedent for having that type of security policy or initiative—