What is the explicit thesis of this book? Is it that the civil war was revolutionary, or is it how the concept of liberty was redefined through this war?

James McPherson does indeed clearly state that the Civil War was revolutionary. However, the redefinition of the concept of liberty was integral to that revolutionary change. In other words, not only did the United States experience significant change, so too did the very concept of liberty on which it was founded.
Arguably, the greatest single change arising from the Civil War was a growing sense of the unity of the United States as a political and cultural entity. Prior to the war, the states were fractured, individual units of power jealously guarding their own political identities and scarcely maintaining a formal relationship with each other. The Civil War changed all that. Lincoln envisaged the union in more substantial terms, in contrast to the largely formal apparatus of governance that had previously existed.
For Lincoln, the union was not simply an end in itself; it was a means of giving expression to the "new birth of freedom" set out in the Gettysburg address. He saw liberty as not just an abstraction, but also as a living, breathing reality in the hearts of men and women. Over the course of the war, Lincoln's understanding of liberty changed. Out of the crucible of this epic conflict a positive concept of liberty was forged, that is the freedom to act unilaterally (albeit still morally). Liberty as inherited from the Founding Fathers was largely conceived in negative terms, that is freedom from rules; in that case, this was largely simply the freedom from British rule.
The new conception of liberty did indeed have revolutionary consequences, not least for Americans' understanding of the appropriate parameters of government action. The American Revolution had been fought against what the colonists regarded as the tyrannical interference of their natural rights by the British government. The experiences of the Revolutionary War inculcated in Americans a deep suspicion of government and the potentially dangerous power it could wield.
Lincoln's positive understanding of liberty, on the contrary, recognized that government, far from being the enemy of liberty, could also be its savior. Under the circumstances prevailing at the end of the war, only a strong, unified federal government could protect and guarantee the rights of emancipated slaves. In doing so, it could breathe new life into the Founding Fathers' original vision.