Deleting a file from a Data Pack will just result in the original not being modified at all, since there is nothing to override it with. Changing the weights in the "start_pool.json" to 0 should work, though there have been reports of modifications to the start pools not having an effect for some reason...
A workaround could be to override the respective town center structures with empty ones instead. Those can be found under "data/pixelmon/structures/gyms/<type>/<type>_gym_tc_<a/b>": https://pixelmonmod.com/wiki/Structure_Editing
The "gym.json" template pool of each Gym village only affects the Gym building itself. Modifying that will still generate the rest of the village, just without the Gym.