When playing with fewer than 5 players, I recommend skipping the "extra loyalty card" rule, even if you are playing with Personal Goals. I rather enjoy having the chance to stick more PGs and FFs into the deck that way.
It just isn't worth playing BSG if there's no Cylon.
If nothing else, you could just use one of the houserules for when there's a YAAC card left, like deduct each resource by one, +1 or +2 on the boarding party track, 4 damage on Gally = victory for cylons, or just play another jump cycle.
And I'd beg to differ on that... we had a pretty epic game where a cylon revealed early in a 5p game. They let me, Boomer out, thinking if I was the other cylon, I would just finish the game sooner. Otherwise, if I were human, I was the only pilot and they desperately needed me out of the Brig. To my surprise, most everyone pitched in to get me out. They were surprised when I escorted civvies. We barely won that game, and even though the lone cylon lost, he got mad props for nearly killing us in a 1 vs. 4 game. Was it unbalanced? Yes. But it sure was neat, including for the cylon. And then you can just house rule such situations as mentioned above.