I never had that problem with a familiar. I played a warlock first time and had my familiar always out (imp), Scratch didn't mind at all and I didn't get dissapproval from my companions. With my beastmaster ranger I had also no problems - spider was always out. That is really strange.
Do you fast travel to camp and them sleep? Or the "Go to Camp to end the day?" Gale had been at camp for me in both instances, but only attacked when I directly fast traveled to camp and it was day time.
