Sneakers/Headscratchers

"Bishop: [The Box] doesn't work, you know. It never did. Abbott: That's not important. What is important is that The Box never existed. None of this ever happened. And I Was Never Here."
 * Ummmm.... why is it possible for Bishop and co to blackmail Mr. Abbot at the end of the movie? Abbot has the guys with guns and the infrastructure to cover up anything he does to them. I get that they don't *have* to shoot the gang, but they can rather than let them blab to the world about the NSA's new toy. Certainly the situation is nothing approaching "having the NSA by the balls". As Crease pointed out earlier - there isn't a government on Earth that wouldn't kill them all for that thing. The NSA is exempt.... why?
 * Because in this movie, our government doesn't kill civilians. When Martin questions Crease about that very statement earlier in the film -- "You said it last night, there isn't a government on earth that wouldn't kill for that thing" -- Crease emphatically adds, "Not ours!" And Crease should know where the US draws the line; he's a CIA veteran.
 * There is also the simple fact that they don't have a damn thing on Abbott actually worth killing them over. Abbott's actions in the movie boil down to two things: a) he hired a scientist to invent a code-cracking device for the NSA and b) he pursued and arrested the thieves who stole the device. Both of these things are 100% legal. The only thing the man is guilty of is doing his job. The fact that the device would be at least as useful for spying on his own government as it is on anyone else's, and the part where he paid for a research project that (as far as the NSA knows) doesn't actually work would be embarassing to Abbott if publicly revealed, which is exactly why he's willing to pay Bishop and co. some discreet blackmail baksheesh in return for them keeping quiet, but public embarassment is the only negative consequence the man is at risk of. On the other hand, if Abbott decides to commit multiple homicides then he is risking spending the rest of his life in the graybar hotel if anything ever leaks, and he's not stupid enough to trade one set of risks for a far worse set of risks in return for little or no gain. Basically, Abbott is proving that he has learned the First Rule of Holes: once you're already in one, stop digging.
 * Highlighted in the end scene itself: