In more recent time during the George W. Bush adminstartion the president was regularly referred to as "Mr." Bush by media commentators. I see no problem with referring to Abraham Lincoln as 'Mr. Lincoln'. It is far more respectful that what I would really like to call him outside of polite company. And by the way, Lincoln wasn't the president of your or my kinfolks who lived during his presidency. So why should I refer to him as President Lincoln?
Lincoln was the Leader of a invading foriegn country as far as the southern Confederacy and those who lived in it were concerned, Jefferson Finis Davis was their President, and I would guess therefore mine since I decended for their prodigy, or had I lived then. Just because they conquered us doesn't make him 'MY' President.