He did what any other head of state would do when faced with the situation of 1861. He did what Jefferson Davis did in the Confederacy. Davis and his crew wanted as much of the US as they could tear away. To be sure they didn't want free states and territories, but they favored doing any damage to the US that they could in hopes that it would further their cause.
So Lincoln supported some temporary wartime restrictions on liberty -- just as Davis did. Just as other war time presidents did. And many of those who were affected were themselves militant supporters of the other side who would do any damage they could to get what they wanted.
One may also note that during the War of the Great Rebellion, that the US Supreme Court held sessions.
Jeff Davis never got around to appointing any justices to the pretended supreme court of the pretended confederacy. He didn’t care much for law, actually. I guess there was a reason why U.S. Grant called one of his horses “Jeff Davis”.