It seems funny that the US could have so feared its existence.
From what I can tell from the pictures, they were probably worried about the fact that CSS Stonewall was an oceangoing ironclad, which would put her in a completely different league from typical Union and Confederate ironclads like Monitor and Virginia (which were basically just coastal gunboats). The Monitor-Virginia duel is correctly famous as the first naval fight between ironclad warships, but it needs to be kept in perspective because both of those vessels would have been hopelessly outclassed by the big oceangoing ironclads that France and Britain had already launched a few years earlier (La Gloire in 1859 and Warrior in 1860). A case in point: sometime after the Civil War, the U.S. Navy made a misguided attempt to send a large monitor-type vessel across the Atlantic to Europe to show the flag. It barely survived the trip, and conditions aboard the ship during the crossing were quite hellish.
I like the part of the article which says that CSS Stonewall was commissioned in January 1865, just a few months before the end of the war. This places the ship among other historical “wonder weapons” that arrived on the scene at the tail end of a conflict, sometimes accompanied by claims that they will miraculously snatch victory from the jaws of defeat – though this doesn’t seem to have been the case here.