a script is like a movie set. it appears complete and real but its really lots of patchwork to make it appear that way (especially over multiple seasons) and if you would move the camera a bit to the right, you would immediately notice that its pretty much just covering the scenes and otherwise ends apruptly. its no encyclopedia which covers every detail.
this smells like a simple hole in the plot and it makes about as much sense as j.d. from scrubs getting run over by a steamroller and suddenly reappearing next week after his funeral, with some vague references to angels by the janitor.
in the ep where starbuck "died" we saw her ship exploding. no uncertanity, no guessing, just bang, which indicates that they really intended her to die at this point. then there was her magical reappearence and this absolutely unlogical wreck on earth with her body in it, which somehow survived the explosion and got teleported there it seems.
either they became desperate because their ratings were dropping or it was a blatant cliffhanger without any kind of logic, "lost" style, which would even more suck. its also no surprice that the producer claims it was always meant that way. sounds a hell of a lot better than admitting that they made mistakes. george lucas did this all the time when he talked about the starwars movies while there were drastical plot changes all the time during shooting them.