Lincoln generally restrained his generals and civil officers, releasing men and allowing newspapers to reopen.
It is fascinating to me that people who get all upset about Ward Churchill's infantile comments seem to think that those actively encouraging sedition and rebellion against the government in the 1860s should have been unmolested.
Lincoln himself, as usual, said it best. Roughly, "Should I hang the young soldier who deserts and do nothing to the deadly enemy of the government who encourages him to do so?"