On his blog, BSG writer and co-exec producer Mark Verheiden writes about how they crafted fake scenes in last season's finale, "Crossroads Part 2" to prevent spoilers leaking out:
The whole process of writing these alternate scenes was interesting. On the one hand, you don't really want to waste much time on something you have no intention of shooting. On the other hand, if the scene isn't at least vaguely convincing, everybody will know it's a ringer and you wind up calling MORE attention to the moment. Further, the cast and crew were going to prep the show, at least at first, off these bogus scenes, so they couldn't be wildly divergent from what we were actually planning.
In this case, we had two revelations to mask. The unveiling of four of the final five Cylons, and the back-from-the-dead reappearance of Starbuck. Now, speaking for myself here, I always assumed that people were more or less expecting Starbuck to come back at some point. But the revelation of the four new Cylons, THAT was going to be the real eye-opener.
So our first bogus scene basically fudged that revelation. Instead of the four realizing they're actually Cylons, they come to believe the Cylons brainwashed them back on New Caprica to (possibly) do bad things.
...So the bogus version closed with a completely invented moment. After the Cylons have reappeared and our pilots are getting ready for battle, Lee rushes back to his quarters to grab a flight suit only to be confronted by Tigh, who promptly conks him over the head with a whiskey bottle (!). Leaving Tigh to wonder if the Manchurian Candidate mechanism had finally been triggered, and leaving poor Lee bleeding out on the floor.
If that had been the real ending to season 3, I wonder what fan reaction would have been?