[Suicide Junkie]

In order to not spin, your thrust would have to be going out in line with your center of mass, and the ship would be basically flying diagonally.

Course corrections aren't really possible when you can't turn right, or even slow down a leftwise turn once you start.

What you'd need is some smaller thrusters on the far side to counteract the torque provided by the main engines.
If the extended arm of the one-sided carrier bay isn't too heavy, (probably mostly open cargo/launch space), you'd only need a small thruster at the end, since torque is force cross (vector multiplication) distance.