In the entrainment example, the frequency of the organ is actually different than the entrainment frequency.
Let's say for instance that a healthy kidney operates at 500 Hz (totally made up number), and a sick kidney will be found to be running at 480 Hz.
By applying an entrainment frequency of 500 Hz, it is the goal to get the kidney to restore itself to 500 Hz.
Each system was vibrating to its own beat; but by being in proximity with each other, they were able to influence and normalize each other.
This is the current concept behind a healing modality.
As for the other effect you had concern with, organs and other large systems are not devitalized by their overall operating frequency.
So far no single frequency within the range we use, has been shown to be able to devitalize a human cell which is many times larger than the pathogens we target.
I would also suspect that the overall operating frequency is the summation of all individual cell frequencies and not the frequency of each cell specifically. Think of it as a more macro frequency that we use when targeting entrainment.
For more details, please check the link: