he is taken out in the novel kicking and screaming and Impy plans his next move as he awaits word of the traitor's beheading. Except in passing by Adama, Baltar is not mentioned again.
The 3rd book The Tombs of Kobol is based on Lost Planets of the Gods. It starts out with Baltar about to lose his head to a Cylon with a BIG axe that the Cylon deliberately sharpens slowly. They're living beings in armor and take pleasure in killing. Lucifer, an ambulatory servant robot and not an IL, stops it and saves Baltar and brings him to Impy (same one, he didn't go boom at Carillon) who spares him.
The 2 eps are better than the books.
The Tv version of the Cylon pulling out and then resheathing his sword is just the footage from the movie version stopping then reversing with Impy doing a new voice over saying later with a stock footage shot of Baltar.
Baltar is not a clone. The difference in that scene between movie and tv release is typical 1978 television.