The method used to destroy the Crystalline Entity, of setting up a resonance harmonic, is a predictably effective way to destroy it, though it seems likely that any such creature would have evolved methods for damping such vibrations.
It is akin to a singer attaining such a perfect and stable pitch that she shatters a glass with her voice. All things have what are called "resonance modes", which is, frequencies of vibration which set up a stable pattern, also called a "standing wave", much like a plucked guitar string seems to be in a fixed pattern due to the resonant wave in it bouncing off one end and returning back in exactly the same time as it takes for the wave to move up and down in one "cycle". If said object is then hit with a so-called "resonant frequency", the energy in the wave is added to the existing energy, and the amplitude, or "height" of the wave increases with the added energy. Continued application of the resonant frequency will cause more and more energy to be dumped into the wave pattern, increasing its amplitude until the object is destroyed.
Probably the most famous large-scale example of this matter is the collapse of the Tacoma Narrows Bridge
in 1940. This concept, of resonance and vibration, is of minor import on Earth, because there are usually a lot of damping (anti-resonance) forces in play. It is, however, of particular significance in the construction of larger, lighter structures such as modern bridges and buildings, and will come much more into play when dealing with structures in space. Considerable care needs to be take when building any large structure in space (including something only as large as the international space station, much less something substantially larger) to add structural entities to actively dampen vibrations lest a resonance be set up from some unexpected source which will treat the structure much as the Tacoma Narrows bridge was treated by the steady wind.
The size of the source does not matter a great deal. Applied "properly", any force is adequate to destroy a structure. Nicola Tesla, the creator of modern power generation systems, as well as defacto inventor of radio, was an expert in resonance. It is said that he had created a device the size of his fist which, when applied and set correctly to one of the structural columns of the building, had the entire building shaking within hours, just by applying a gentle tap over and over and over to the column it was attached to. A similar thing could happen to a space structure -- a small motor vibrating just right in just the right location could set up a vibration which would destroy the structure, if there wasn't proper and adequate vibration damping in place to stop it. This is, in fact, considered an actually serious, major obstacle to the creation of an SF-style "space station". We do not understand such problems adequately to be sure we can deal with them properly.
In this same sense in this episode, the doctor's machinations created such a destructive force in the Crystalline Entity, by going tap-tap-tap, "just so", until it shattered from the slowly building energy in the standing wave.