My gut feeling is that with a couple changes this episode would have hung together better-

1. Have them take a shuttle instead of the Enterprise. This lowers the stakes for our command crew and simply makes more sense than half the crew (that wasn't on leave) agreeing to steal a ship. It also means they need to figure out a different way to deal with the fake Federation ship at the end of the episode is some way other than 'shoot it with bigger guns'
2. Have Chapel and M'Benga do something within their character strengths to escape instead of magic drug that lets them hand-to-hand fight their way through a dozen or more Klingons.

That said, there were a lot of things I DID like about the episode, including the Klingon Captain at the end and the new Chief Engineer.