Well, you just blasted one of the most revered episodes in all of Star Trek.
A couple of things to get used to. Bad people will take over the ship all the time. They'll take off with shuttlecraft all the time, too. It's just part of the game. Without all of these thefts and hijackings you lose a lot of potential, yet important plot devices. Here's something you'll definitely be seeing a lot of:
Sir, I'm detecting an unauthorized launch of a shuttlecraft.
Stop it. Close the bay doors!
Too late sir, he's already gone.
Get a tractor beam on him!
He's just out of range, sir.
Beam him out of there!
too late sir, he's got his shields up now.
Oh, and people will beam off the ship without authorization, too. The simple truth is that if we were to believe that ship's security were at all passable there wouldn't be many stories to tell. Best not to dwell on it.
As for Khan, the subplot with McGiver was pretty silly. I always thought she flipped out way too early. But letting Khan go was pretty reasonable (for what we know up until now, at least). He was a genuine badass, and not inherently evil; just ambitious. Plus, if you think about it, he and his goons would probably be damned difficult to imprison. Leaving them all stranded on a deserted planet was as good a strategy as any at that particular point of time.