Actually, a search of the JOURNAL OF THE CONFEDERATE CONGRESS (available online), for "Chaplains in the Navy," shows that the bill to appoint them was approved by President Davis, and passed in December, 1861, though certainly none were ever appointed.
When you get to the JOURNAL OF THE CONFEDERATE CONGRESS web site, do a search under the heading "chaplains in the Navy," and you will come up with several entries. These show the motions being put through, voted upon, and being finally accepted.