I view the order of events simply as this:
1) Starfleet finds Botany Bay, realizes what it is, thaws Khan, since he has a violent, military mind - he brought something to the table that other Starfleet engineers didn't have - a killer instinct. Yes, his tech knowledge is VERY out-of-date, but if his intellect is enhanced, there's nothing to say he couldn't have been educated on tech. With a digital library at Khan's disposal who knows how much info he could absorb?
2) Khan develops lots of things for Starfleet, not just the missiles. That big ship that Admiral Marcus had was also from the mind of Khan - again - Starfleet had ships for exploration and peace. Sure they have defensive capabilities, but this ship was offensive FIRST. Maximum damage, minimum crew.
3) Marcus wants to start a war with the Klingons, he gets Khan to develop long range missiles that can be fired from outside the neutral zone directly at the Klingon Home World. Khan uses this as a way of smuggling his crew out of the Starfleet facility where they are being held and starts putting them inside of the missiles, shielded so as to avoid them from being scanned.
4) Marcus discovers Khan's plan and moves in to stop him. Khan escapes. Marcus knows that there are Botany Bay crew members in those missiles and he doesn't care. Ultimately he doesn't care if all 72 of them are fired on the Klingon Homeworld and decimate a good portion of it - all he wants is a war, started by the Federation, against the Klingons. He's like Dick Cheney.
5) Khan attacks the tech archive in London so he can grab the experimental transporter based on Scotty's equations so he can attack Starfleet headquarters and then beam himself to the Klingon Home-world, knowing that if he goes to there, Marcus will use the missiles to fire on the Klingon Home world from Federation space starting the war he so desperately wants
So from here there are two possibilities and since they are not mutually exclusive of each other, it's possible both are true:
6a) Khan developed a fail-safe into the missiles where he could deactivate the explosive yield, alter flight trajectory and even stop a missile in flight, so even if the Starship Captain that Marcus sends after him DOES fire the missiles as ordered, Khan can deactivate them, have them stop somewhere in the neutral zone, steal a ship and go claim his crew - Khan wins
6b) Just in case the Starship Captain that Marcus sends after him DOES NOT fire the missiles as ordered, he knows he can simply wait to be collected by that Starship's Crew knowing full well that his entire crew will be on board. Possibly even gaining sympathy from that ship's Captain and then the events pretty much following a similar story of the Space Seed episode where Khan and his crew try to take over a Starfleet ship. If that's successful - Khan wins.
And in the movie we see the result of the 6b option unfold and the only place where Khan's plan goes "wrong" is that Kirk doesn't entirely act in a manner that Khan expected.
So what I'm trying to say is that Khan, hedged his bets - he forced Marcus' hand so that no matter what actions Marcus and the rest of the Starfleet took, he could see a positive outcome for his own goals.
Is it possible that Marcus could have just destroyed all of the weapons. Sure.
Is it possible that Starfleet could have taken all of the Botany Bay crew out of the tubes. Sure. (in this scenario, if Khan has the ability to control the missiles himself, he could easily stop the missiles, steal a ship, gather the missiles and then threaten to fire them at Earth - again Khan wins)
Yes, I understand that no where in the dialogue of the movie do they imply that Khan had built fail-safes into the missiles to protect his crew, but no where does the dialogue say "dismiss Khan's plan as being stupid" either.