In the BATTLESTAR GALACTICA faux-feature-film they killed him (albeit off-camera).
In Saga of a Star World, they gave him another chance to lure humanity's survivors to Cylon-induced doom.
In MISSION GALACTICA: THE CYLON ATTACK, he just reappears inexplicably leading the Cylon task force (with his very own Cylon-style helmet).
Marvel comics seemed less sure what to do with him.
In the BATTLESTAR GALACTICA SUPER SPECIAL, based on the pilot's shooting script, they killed him off in graphic detail:
When the same material was reworked for issue 2 of the regular Battlestar comic book (prepared and published later), Baltar's fate was less clear. And they gave him hair:
Only to kill him off again (trapped in the wrecked tombs of Kobol, which he escaped off-camera in the TV version) in the opening pages of Issue 6, the first storyline not to directly adapt TV material. Baltar would, of course, appear throughout the single TV season (albeit confined to the Prison Barge from mid-season):
The original plan was indeed to execute Baltar in the Imperious Leader's throne room (numerous takes on the bloodless execution can be found in the deleted scenes section of the Battlestar Galactica DVD box set but it seems that nothing approaching the gore of the Marvel interpretation was ever shot).
During shooting and editing of the pilot, the decision was made to extend ABC's order from three TV movies (Saga Of A Star World, The Gun on Ice Planet Zero and Lost Planet of the Gods) to a full weekly series.
This necessitated some changes to the cast and format of the weekly series and the decision was made to retain John Colicos as the recurring Cylon leader. A new coda was added to the pilot episode, explaining why the new Imperious Leader wishes to retain his services and introducing Baltar. This was likely shot later, possibly during production of one of the subsequent episodes. A re-edited (changing Baltar's assignment somewhat) version of the scene also appears in Lost Planet of the Gods.
The coda was omitted (and possibly wasn't even shot at the time of release) from the international theatrical prints of the pilot episode (released in UK cinemas in the summer of 1978, some two years ahead of the broadcast premiere of the TV show) leaving Baltar's subsequent redemption, resurrection and leadership role in the sequel MISSION GALACTICA: THE CYLON ATTACK (assembled from the TV episodes The Living Legend and Fire in Space) completely unexplained.
Baltar also appears in the third, and final, Battlestar feature film CONQUEST OF THE EARTH despite the character never appearing in GALACTICA 1980, the shoddy TV sequel where all of the Conquest content is otherwise derived from. Baltar, Lucifer and Spectre all appear courtesy of partially redubbed footage from the original series episode The Young Lords.