The simplest brief answer is that the south LEFT the Union to preserve slavery. This is obvious in their constitution. Lincoln initially wanted to preserve the union, and made his famous statement "If I could save the Union without freeing any slave I would do it, and if I could save it by freeing all the slaves I would do it; and if I could save it by freeing some and leaving others alone I would also do that." Ultimately the demands of the war lead to the emancipation proclamation, but even that was carefully calibrated to 'areas in revolt as of Jan 1 1863'. So technically (for instance) slavery was still legal in states such as Maryland until the 13th amendment passes in 1864.

To add a bit to previous answer, Lincoln did not have the authority to simply free all slaves. They were still considered property. Which is why the wording is so specific. He could free those slaves in areas of revolt, since the federal government was taking control of those areas.