I have one of those also, if it looks like this ...
and it can be noisy!
If you park the engine in neutral and just vary the voltage, the rotation speed changes dramatically with track voltage (on mine.) At higher voltages it sounds like metal against metal, and looks like it could fly right off the car. Fortunately my Williams engines don't need much voltage, so no real issue for me.
That said, I haven't tried any cures, but I can think of two things to try:
Normally I try the cheapest thing first, but in this case I would try the easiest thing first. If you have a 2nd rubber ring, stack it on top of the first rubber ring. I would try stacking them both ways, with the two rings stacked flat side to flat side, and then both of them with their little feet facing upward. The increased distance from the coil to the base of the beacon might be just enough to settle things down. Or it may not even rotate any more. Like I said, I haven't tried this.
The other idea is to stick one or two diodes in series with each other and put them in series with the car's coil circuit only. On that car, it's not too hard to get to just the coil wires - if memory serves, you can easily access them under the black plastic engine shell. But before you go the work of cutting wires, soldering and heat shrink, I would first test the solution by placing the car on a short test track, unscrew the bulb and place the diode(s) in series with one of the two track feed wires. Do not use any caps to smooth the half wave DC, or you will get NO vibration. It's possible this solution could work … or kill too much of the vibration since you are now powering the coil with roughly half the voltage, hence this quick and easy test first.
I hope one of those works!