Liability (spoilers)
So, they go through all this trouble to keep Jennings from knowing what he's working on or at least telling other people about it. I mean, when an NDA just isn't enough there's always brain damage right?
Jennings, however, is a genius and is paid handsomely for it. What about all these grunts with guns, on the other hand? Guns they obviously weren't trained very well in how to use. Do you think they're bringing home the big bucks? What's more likely, that a key player in your entire operation is going to spill the beans despite his 90 million dollar paycheck, or an undereducated gun toter is going to start blabbering about a very peculiar machine while drinking at a bar one night? Then multiply that by a least 50 (I didn't really count how many grunts there were) and you really start to wonder.
I realize it's a plot device, but it's kind of annoying that it basically forces you to believe that everyone working for this corporation is inherently evil and the "bad guy" and not just some Joe working a 9-5 job.