Let's keep in mind that, in the film, Section 31 built a massive military starship, in secret, and that Adm. Marcus used it to try to destroy Enterprise when it didn't do what he wanted. Shades of the CIA, the Pentagons "black ops", or whatever, take your pick. Allegorically of course.
I've rewatched the film recently and this aspect is central to the subplot. I reckon if it was the actual plot, without Khan, it might have been a better plot for the film. But hey, state secret. ;p