I am not inclined to look at the quotes from St Agatho and the Sixth Ecumenical Council from a myopic perspective but from a view based on the communion of saints, since a legal perspective would be contradictory.
Clearly, both quotes are referring to the Roman Church and her head, St Agatho. But the Sixth Ecumenical Council also condemned Pope Honorius of Rome as a heretic in the same letter of the Council:
And then tearing to pieces the foundations of their execrable heresy, and attacking them with spiritual and paternal arms, and confounding their tongues that they might not speak consistently with each other, we overturned the tower built up by these followers of this most impious heresy; and we slew them with anathema, as lapsed concerning the faith….and their names are these: Theodore, bishop of Pharan, Sergius, Honorius, Cyrus, Paul, Pyrrhus and Peter. (Migne, Pat. Lat.,Tom. LXXXVII., col. 1247 et seq).
So to simply take a literal reading of whether the Church had always followed Rome (a "yes" or "no"—Rome or not) would indicate the Council contradicted itself. I am more inclined to qualify the statement in the context of the Orthodoxy of the Roman See, so as the actions of the council make sense. In a historically honest context, I find these statements agreeable, which make no claim of any sort of jurisdictional primacy or Divine right, but recognition of the Unity of Faith between Pope St Agatho and the Prince of the Apostles.
I’d like to address the issue of the Libellus of Hormisdas. You said that referring to the issues surrounding the document as a "sorry affair" could only be viewed as such by the devil. I decided that this issue obviously deserved some research. That research leaves me a question-- the answer I am sure you can glean through the sparse documentation of the period.
Why did the Patriarch John II object to the Pope’s letter-- and only agreed to sign it after a council with the Papal legates present, by re-writing the letter with a preface stating: Know therefore, most holy one, that, according to what I have written, agreeing in the truth with thee, I too, loving peace, renounce all the heretics repudiated by thee for I hold the most holy churches of the elder and of the new Rome to be one; I define that see of the apostle Peter and this of the imperial city to be one see, and at the same time, why did Dorotheus of Thessalonica (you allege Thessalonica was once the vicariate of Rome itself) rip the document in half? It should also be noted that the legates accepted Patriarch John’s revision, and that despite the protest of St Hormisdas, Dorotheus was tried and freed in Constantinople after writing Hormisdas a letter affirming Chalcedon (Inter Epp. Hormisd. Ixii.lxiii. lxxii. Lxxiii). Putting my statement in such a context, I think calling it a "sorry affair" makes sense. But you say otherwise.