nutation dampers
A piezoelectric system would have faster responses than moving weights.
In a rigid-truss dumbbell ship, ideally main thrusters would be in the middle of the truss, maybe even counterspun. Timing spinning thrusters would not be difficult.
The point is if you're trying to get past "plant the flag" missions, you need an infrastructure where you can build things in orbit and set up the kind of systems that will really do the job right.
In the late 50s and early 60s, it was always assumed that this would be the way we'd do things. In Willy Ley's books, the first lunar lander was about fifty feet tall, and assembled at an orbiting space station. It's still a good idea.