The rocket analogue of a flywheel is a very heavy rocket, whose large inertia would smooth the changes in its velocity due to propulsion pulses.
Nevertheless, this solution is undesirable, because it would limit the acceleration of the rocket to small values.
The right solution is that mentioned by the other poster, i.e. to have a large number of pulsed rocket engines, whose pulses should have distinct phases. In this case there should be pairs of engines with synchronized pulses and symmetric positions, to avoid the rotation of the rocket, because the engines can no longer be aligned with its center of inertia.
An Orion drive actually scales pretty nicely. As I recall, a city 20 miles wide planted on top of a big metal plate was just about the sweet spot. Mostly this works because it is easy to make a bomb with more yield without making the bomb larger.
I have this amusing vision of a rocket ship that resembles a Slinky™ dog, the rear propulsion section connected to the habitable front by an exaggerated spring.
More likely you’d have the engines flying out in front on tethers, so like a skier behind a thermonuclear ski boat. Tethers would weigh a lot less than springs.
You could also have fully electromagnetic “springs” using powerful superconducting magnets.
I was going to just say springs, but this is more accurate. Orion (the original nuclear rocket) already had this. I'm not sure if the complexity of the multi-chamber pulsed plasma would make dealing with the vibrations more challenging though.
