Khan was trying to run a ship usually crewed by at least 300 with a crew of about 60. Even Enterprise with a full (admittedly mostly cadets/trainees) crew faced huge damage-control issues.
Where are those numbers from? not that it matters much, the next movie canonized that a chimpanzee and two trainees can run a starship.
After being modified by Mr. Scott. And even then it was useless in combat.
Not only that, the commander of an enemy ship with about twelve men thought they could board and overtake it.
They had surrendered. They weren't expecting to fight their way to the bridge or anything.
300 seems a fair estimation, based on the Enterprise
having about 430, and the Reliant
appearing to have a slightly smaller overall mass than her.
Scotty automated the ship. A chimpanzee and two trainees could probably fly her from A to B, but there's no chance to repair any damage anywhere on the ship apart from the bridge, do any routine maintenance, or even operate the thing effectively for anything above about 36 hrs tops!
As for 12 Klingons capturing the Enterprise
, firstly Kirk had surrendered, secondly they had hostages to ensure compliance, and thirdly Kruge was a complete whacko!
"We are Klingons!" hardly guarantees victory when facing 30-1 odds and fighting on the enemy's home turf. Had Kirk had a full crew and intended fighting them, the Klingons would have not even got out of the transporter room.
A moot point though, as a fully-crewed Enterprise
would have been able to raise shields and simply blown the Bird of Prey into scrap anyway.