Unlike PETA, if Team Plasma actually managed to create separate worlds for people and Pokémon, there's sufficient evidence (the Mystery Dungeon games) to suggest the Pokémon would do just fine on their own.
In reality, if all the animals working and living with humans were released into the wild, they wouldn't last a week. Either they'd be eaten by predators or be stricken by one of the many illnesses that are normally kept at bay by human-developed medicine.
The whole PETA/Team Plasma comparison falls apart when you remember that Pokémon have human-level intelligence and the power to bend the seventeen elemental to their wills, and are generally good at heart, whereas in the real world most animals are nowhere near as mentally capable as humans, and the second smartest animals after humans, dolphins, are Ghetsis-level dicks, and the rest of the animal kingdom is neutral at best. Except for elephants, one of the few truly altruistic animals there are.