That's not a true picture.
"Scholars still debate whether Lincoln had the authority to invoke the Constitutional provision suspending Habeas Corpus during the early days of the war. I will not wade into the muddy waters of that debate. I am more interested in talking about what Lincoln did after March of 1863--for that is when Congress gave Lincoln legislative authority to suspend the writ. From that point forward, Lincoln faced no constitutional obstacles. He could arrest whomever he chose, without courts interfering with Writs of Habeas Corpus. What did Lincoln do at this point? Did he attempt to stifle political debate, by imprisoning his opponents? In short, did he trample on the civil liberties the Writ of Habeas Corpus was meant to protect?
A recent historical study, entitled The Fate of Liberty, says "no." The author, Mark Neely, combed through the musty boxes of arrest records from the Civil War "to find out who was arrested when the Writ of Habeas Corpus was suspended and why." Neely concludes that, throughout the war, Lincoln was guided by a "steady desire to avoid political abuse under the Habeas-Corpus policy. According to the best estimates, about 38,000 civilians were arrested by the military during the Civil War. Who were they? Almost all fell within a few categories: "draft dodgers, suspected deserters, defrauders of the government, swindlers of recruits, ex-Confederate soldiers, and smugglers."
And strikingly, most of these were Confederate citizens, caught behind Northern lines. The numbers show that very few civilians were taken from their homes and arrested. And of those few arrests, only a handful were colored by political considerations."
-- Justice Sandra Day O'Connor, 11/19/96
Walt