Isolation allows for whomever is doing the isolating to control the environment completely, and modify it to their own benefit. This is exactly what "re-education" camps have done throughout history; providing confinement to a specified group for the purpose of brainwashing them to the dictator's preferences.
A similar process is at work in the allegory of Animal Farm. Although not re-conditioning the puppies, Napoleon, as dictator, is conditioning them from nearly birth -- isolating them and establishing an environment where he can instill their complete loyalty and obedience to him alone. Isolation is key in the process, as it forbids any external reference the pups may come across in their development to challenge the established order of things. If they were not isolated and did not have a frame of reference imposed upon them, they could possibly learn to think for themselves and question the authority.
When the time was right, Napoleon, like all dictators, used his armed automatons to maintain and expand his power.