It sounds like there could be two things happening, but both are related. The grado is a high complience cartridge, which means it has a less stiff movement in the cantilever assembly. If the arm is too heavy, it will not move fast enough with the cartridge allowing the cartridge to transmit subsonic frequencies. (in short, the resonent frequency of the arm/cartridge is too low). Also, or in addition, the turntable could be picking up low frequency vibrations, and transferring them the same way.
Most quality arm and cartridges made today are designed to have a resonent frequency in a higher range so this does not happen, because when it does, sound quality suffers. In addition, better pre's and phono's do not have sub filters because they degrade the signal, and are also not nessessary with a properly set up arm/cartridge.
The arc you are considering is a good pre- and if you are willing to spend that money on one like that, it would be more wise to spend money on the turntable in addition rather than trying to find a quality piece that can handle the shortcoming of the table. Trying to mask the problem by spending in equipment to cover it vs. spending on equipment that doesn't have a problem to cover. Filters like mentioned above are not a nessessarally bad idea, but it would be worth considering the cost of adding vs. upgrading.
Also, it seems most mac's have a tendency to add to the bottom end, so that might be another thing to consider. If you are using a mac, it could be exaggerating the problem.
The other part of your dilema is possibility of damage. The woofer movement you are desribing is only a risk if the speaker is overextending itself and bottoming out or working too hard and overheating. Woofer pumping is more common than damage from it, so if things are sounding good to you and the speaker is not bottoming out, it might not be a 'problem' you need to solve.
I hope some of this helps.