There is no doubt what-so-ever that the progressives have used, and continue to use, that fact to great effect!
Breaking it down, you are saying that Lincoln, by fighting to preserve the Union, made the Union more powerful than the states.
Your position, however, begs the question of whether the states were allowed to secede. If they were not, and it is debatable, then Lincoln certainly had the right to fight a war to maintain the Union. You can't complain that to defeat an illegal war, he defeated the states who illegally left the Union.
Whatever the rightness of the secession issue (and it is incapable of decision because, like many human endeavors based upon interpretation of words, there is no "correct" answer, only opposing theories), Lincoln also had the moral high ground in that war, and in preserving the Union, laid the groundwork for all the good things that a united nation was able to accomplish in these past 145 years, not to mention eliminating the evil of slavery.
If it was a debate that could go either way, and one course leads to indefinite extension of an evil system and long-term warfare between two neighboring states, and the other results in a final resolution of a long simmering issue and elimination of a terrible evil, I would take the latter every time.
Having taken the latter approach, all that was established was that a state could not secede. Not that a state could not regulate its internal affairs. That was not a principle that Lincoln or the Republicans established. The Constitution was amended in two key aspects, eliminating slavery and requiring that all US citizens be given due process of law. Period.
No principle detracting from federalism, any more than the Bill of Rights already did, was established by the example of the Civil War. Federalism didn't die until the Democrats, the second generation descendants of the southern slave-owners and their northern sympathizers, decided to use the power of the state to establish socialism in the United States. Southerners were eager to join a coalition with Northern Democrats because, in spite of the socialist aspects, it gave them protection in their home states and allowed them to maintain their in-state fiefdoms for a few decades more. The slaves by then had become little more than serfs, not much different than before they were supposedly freed by the 13th Amendment. Those Democrats, the Northern socialists and their southern racist allies who descended from racist confederates, are the cause of our ills today. You are their progeny. I remain their opponent.