But like if Equestria doesn't give two tits and a gravy about Sazkarjhia how come it's when they're trying to quell an insurrection that could get out of hand that they're like "Oh better be all righteous and shit and give them religious freedom."

They didn't just leave, they staged a Coup d'etat, which is considered a crime against the state in Sazkarjhia.