And yet, when President Jefferson suspected his own former Vice President Burr of planning to take over Louisiana and declare its secession, Jefferson had Burr tracked down, arrested and tried for treason.
So, declarations of secession were far from trivial matters in Jefferson's eyes.
Indeed, your quote from Jefferson above merely conforms to one of the two conditions all Founders said were necessary to justify declarations of secession:
The absence of such justifications our Founders considered to be secession "at pleasure" which was not justified by any, and could fall into the constitutional categories of rebellion, insurrection, "domestic violence", invasion or treason.
I would point out that one man plotting to subvert the Interests of the Government of which he is a part is a very different thing that many millions of people voicing their desire to separate from a government which no longer serves their interests.
Major Breach of Compact -- usurpations, oppression or injury.
I think we have already established that depriving people of "rights" which were explicitly enumerated in the larger body of the US Constitution, constitutes a breach of compact. The Refusal of states to return escaped slaves is a breach of this clause in the constitution. The efforts of the Government to ban slavery in future states would also be regarded in this light.
So even by your standards, what the Union was doing did constitute a "Major Breach of Compact -- usurpations, oppression or injury." You may not agree with this constituting an injury, but that is because you are looking at the "injury" with 2015 eyes, instead of 1860 eyes. According to the laws of that time, this was an "injury" and breach of compact.