There is no doubt that prejudice and reservations against other kinds do exist in the Great Valley. However, I would rather see Chomper's treatment in the Great Valley as a perfect example of how prejudices are overcome rather than fostered there.
Think of it, knowing what Chompers is and what he is bound to become and with the awareness of that he won't be able to live on "buzzing stingers" for the rest of his life it would not even be a mere prejudice if the GV inhabitants decided not to permit him there. Such an action would be based on solid information and sad but necessary risk calculation rather than mere prejudice.
Unless the GV inhabitants are tolerant enough to allow Chomper to eat the corpses of those of them who die a natural death (always "hoping" that they will die on a basis regular enough to sustain Chomper), the day was bound to come on which Chomper would either starve to death (unwilling to act upon his nature and attack anyone), leave the Great Valley for good (to hunt those whom he doesn't know), or (least likely in my opinion) attack anyone with his natural instincts winning over his friendship.
Some species seem to hold less prejudices than others (e.g. Ducky's family accepting Spike without any question) while Threehorns seem to hold particularly strong prejudices (here is a
thread which may also be of interest in this context). In some cases the prejudices may be justified to some degree (at least nobody ever contradicted the claim that clubtails are smelly; an estimation expressed even by open minded Ducky).