Throughout history and into the present, government restriction on civil liberties has almost always been proven unjustified.  During World War I, there was no really organized opposition or significant spy rings, or afterwards, any communist conspiracy.  A government crackdown was not warranted.

In World War II we interned 120,000 Japanese-Americans, citizens, out of hysterical fear, to no good end.

As a nation, we tend to do foolish things with our freedom when we are afraid.

Why not? Marriages dissolve; why not countries? People can divorce, but states cannot secede?  My wife wants to leave, but I decree its in the best interest of the family for her to stay, and force her to do so? And when she moves into another house against my decree, I break in and drag her by the hair back to my own? Certainly no one would condone that for individuals; why so for nations?

Yes, the existence of the United States was threatened.  Maybe its death would have birthed two new nations, the Confederate and Federal States of America, and not a drop of blood needed to be shed.  Instead, the bloodiest conflict the United States has ever seen resulted in over 600,000 casualties and a dead president.

As to whatever motives that drove President Lincoln to do what he did, what he did was unconstitutional. Understood, he did not make those decisions lightly, and he certainly thought he was acting in the best interest of the country, but that alone is not justification for expanding Presidential powers and acting illegally.  If we are to adhere to the Rule of Law it means that no one, and no excuse, supersedes it.  Perhaps Congress in the 1850's, as the nightmare was on the horizon, should have considered enacting a process by which states could leave the Union; better yet, perhaps the Founders should have written in an "exit strategy" in the founding document at the beginning.

In case you're wondering, I'm born and bred and live in New England.  And those six New England states were the first to think of seceding way back in 1807, after the Federal Government destroyed the Northern economy by closing the ports and shutting down trade!

Certainly, voluntarily remaining in the Union was (is?) the best option.  What's objectionable is forcing the Union on an unwilling party.

Had we let the South go, perhaps we wouldn't have an onerous Federal Government today.

A wrong idea begets wrong practices.  Lincoln suspending  habeas corpus and dissolving Maryland's legislature (so they wouldn't vote to secede) was patently unconstitutional and a grave abuse of presidential power.  His actions stemmed from his belief of preserving the Union.  However, there are those who argue that since the Southern states joined the Union voluntarily, and they voluntarily choose to withdraw from the Union, they should have been peaceably allowed to do so. National emergency solved.

Throughout history, leaders have used warfare as an excuse to undermine the liberties of the people.  Sadly, the US is no exception, most grievously during the prior presidency.  Suspending habeas corpus expands the power of government, in those cases, to hold secret trials.  Of course, an exception like a  "national emergency" may require stringent methods to respond to the emergency,  but this suggests a bit of shutting the barn door after the horse has fled -- such measures do nothing to solve the "emergency," (by the time government responds the emergency is over) yet they erode liberty.  It's a show of force to convince the people government can do something, and that something is to expand its own power.  Fortunately, when when bad laws or decisions have been committed, they have in short order been rectified, and not persisted permanently. Yet.

It has been quite common for the government of the United States to restrict individual freedoms during wartime.  The courts have consistently upheld the power of the government to do so during national emergencies.

I also agree that suppressing individual freedoms and increasing the power of government is almost always a bad idea, with negative consequences in history.

To play devil's advocate, during the Civil War Lincoln was especially restrictive on the freedoms of people to dissent and/or preach secession, up to and including arresting and imprisoning the Mayor of Baltimore and most of the city council without trial or charge.  Didn't he have to do so in order to preserve the Union?

I would not argue that World War I represented an equally grave threat, however.

The second link below is an article rating several presidents on civil liberties, including Woodrow Wilson.

I assume you are talking about the Espionage and Sedition Acts passed during World War I.

I do not believe that those acts were justified.  In fact, I do not believe those acts would have been warranted in any circumstances.  The acts made it illegal to say or do anything that could be construed as opposing the war or the government.  That led to such things as Eugene V. Debs being imprisoned for opposing the draft.

It can never be appropriate for Americans to be banned from expressing their opinions.  It is one thing to ban actions that would hinder the war, but banning speech is unAmerican.