Seems like Lincoln is still without controversy, but maybe going a little further back we can find an action against a government that is less controversial. In addition, perhaps we can find the germ of Lincoln's justification (and the outrage of those who have opposed his justification) in the words that launched the United State of America as a nation:
When in the Course of human events it becomes necessary for one people to dissolve the political bands which have connected them with another and to assume among the powers of the earth, the separate and equal station to which the Laws of Nature and of Nature's God entitle them, a decent respect to the opinions of mankind requires that they should declare the causes which impel them to the separation.
We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness. — That to secure these rights, Governments are instituted among Men, deriving their just powers from the consent of the governed, — That whenever any Form of Government becomes destructive of these ends, it is the Right of the People to alter or to abolish it, and to institute new Government, laying its foundation on such principles and organizing its powers in such form, as to them shall seem most likely to effect their Safety and Happiness. Prudence, indeed, will dictate that Governments long established should not be changed for light and transient causes; and accordingly all experience hath shewn that mankind are more disposed to suffer, while evils are sufferable than to right themselves by abolishing the forms to which they are accustomed. But when a long train of abuses and usurpations, pursuing invariably the same Object evinces a design to reduce them under absolute Despotism, it is their right, it is their duty, to throw off such Government, and to provide new Guards for their future security.
What this remarkable statement says is that the British government systematically and sustainedly denied the people of the colonies to what it calls "unalienable Rights" endowed by man's Creator. Because the previous Government was not constructive, but "destructive of these ends", it became necessary for the colonies "to dissolve the political bands which have connected them with [Britain]". It's not explicitly stated here, but the colonies did not have the power to alter the previous Government and therefore was left only with the power to abolish it.
It appears that the Southern states saw the US Government in much the same light as the Founding Fathers saw the British Government. It seems that Lincoln did not see things that way. His most well-known, and perhaps best, statement of his position on the war comes from his Gettysburg Address:
Four score and seven years ago our fathers brought forth on this continent, a new nation, conceived in Liberty, and dedicated to the proposition that all men are created equal.
Now we are engaged in a great civil war, testing whether that nation, or any nation so conceived and so dedicated, can long endure. We are met on a great battle-field of that war. We have come to dedicate a portion of that field, as a final resting place for those who here gave their lives that that nation might live. It is altogether fitting and proper that we should do this.
But, in a larger sense, we can not dedicate -- we can not consecrate -- we can not hallow -- this ground. The brave men, living and dead, who struggled here, have consecrated it, far above our poor power to add or detract. The world will little note, nor long remember what we say here, but it can never forget what they did here. It is for us the living, rather, to be dedicated here to the unfinished work which they who fought here have thus far so nobly advanced. It is rather for us to be here dedicated to the great task remaining before us -- that from these honored dead we take increased devotion to that cause for which they gave the last full measure of devotion -- that we here highly resolve that these dead shall not have died in vain -- that this nation, under God, shall have a new birth of freedom -- and that government of the people, by the people, for the people, shall not perish from the earth.
Here, Lincoln seems to justify the civil war as necessary on the same grounds as the Revolutionary War was necessary. He seems to take the earlier Declaration of Independence as higher priority than the Constitution, which came later. He certainly played hard and fast with the rules, if he didn't violate his constitutional powers outright. He justified himself (whether rightly or wrongly) by appealing to a higher rule: "that government of the people, by the people, for the people, shall not perish from the earth."
So I think a legitimate grounds for violating a rule is in the service of a greater rule. That's why the police are allowed to speed and double-park when pursuing criminals.