Yes, in the early Church, communion with the Pope was the norm, but that communion was not as widely understood as it is today. The problem during the Three Chapters Controversy primarily surrounded Emperor Justinian’s ruling which was unprecedented at the time, not in the case of an Emperor proclaiming the anathema, but a postmortem anathema being issued in the first place for those who died in the good graces of the Church. As the proclamation was issued by the Emperor, not the Pope, and was simply accompanied by the Tome of Leo, it was seen as by some as the Pope’s personal assent, not an authoritative teaching. By the time the Pope’s authoritative position was made clear, the Schism had already been set in motion and a new excuse was formulated that the Pope’s words on the subject couldn’t be authoritative in this case because it contradicted the Eccumenical Council of Nicea (which it didn’t actually do).
