This is the best that I've heard this expressed. While I've known this for a number of years, I never learned it in school, and expect that very few Americans do.
This is a classic example of the post hoc ergo propter hoc (after this therefore because of this) fallacy.
Lincoln did what was necessary to win the war. After the war, with the exception of Reconstruction, the relationship between the states and the federal government returned to pretty much where it had been before.
It wasn't until the Progressives of the late 19th century and in particular TR got going that the federal government began its continuous march to power. This was 25 years or so after Lincoln. To blame everything bad that has happened in this country since 1865 on Lincoln requires us to assume the Progressives wouldn't have come along if Lincoln had acquiesced in southern secession. This assumption is based on absolutely nothing.
We must also assume that two nations, inherently hostile to each other, could have co-existed on this continent without necessarily increasing government power in each. Given the massive increase in government power, complete with huge standing armies, that took place under similar circumstances in Europe at the same time, this seems a remarkably inapt assumption.