How long do you think pro-Nazi newspapers would have been allowed to publish after Pearl Harbor? More importantly, do you think they should have been allowed to do so?
I don’t believe German newspapers have U.S. Constitutional protections.
I don't believe that was ever an issue. And there does seem to be a major difference between being on the side of a foreign country in a war and taking a side in a domestic dispute that represented over nine million Americans (the CSA states' population at the time.)
Regardless, I probably would ignore it. Rights are for everyone; it's too slippery a slope to let the government ever get its foot in the door deciding what is and is not acceptable.