The Eleutheroi-hating AI is probably hardcoded into the M2TW engine. After all, in vanilla the Rebels were religious heretics/pagans rebelling against the Pope, so the Pope hated them, which made all the Christian factions hate them and seek to get into the Pope's good books by wiping them out and ending their heresy.

With this in mind, I agree the Eleutheroi garrisions should be made into full or nearly full stacks everywhere.