I'm not an expert
Nope, just about as far from it as you can get, so there may already be soemthing out there like what I'm going to describe and I just don't know it.
At a corporate level, is there something that would take a baseline of a system, and periodically compare that baseline to the current state? Then if you added an approved software, or installed an approved update, a new baseline is taken?
Of course, that wouldn't necessarily help with Flame, since it had a Microsoft certificate, it probably came through approved channels.