I've never understood the concern about .45 ACP overpenetrating. A big, slow moving bullet is less likely to overpenetrate than a faster moving bullet (9mm, .40 S&W, etc). This is true in HP ammo, and it's also true with hardball, where a 9mm ballistics profile looks like an ice-pick stab wound.
As for me, in the situation you describe, I'm not sure the choice matters. You have been awakened and are alert. The intruder is unaware you are awake and armed. You've got the tactical advantage and caliber is not of primary importance.