The original TV version is the longest version.
The one that was released in the movie theatre is shorter and is the one that shows Baltar being killed.
I've seen in the TV version, just as the centurion is about to behead Baltar, Imperious leaders voice is heard ordering it stopped saying " he may yet be of some use to us".
In one of the novels, Baltar is lead away to an execution chamber. Lucifer has convinced Imperious leader that Baltar may still be usefull and he is spared that way.