My safety is my brain. It rarely fails.
Now that's a much more interesting statement than it might appear to be. The question is, what part of your brain?
In the seconds after being rudely awakened, are all of your cognitive abilities functioning fully? Very few can say that they are. While you're trying to shake the cobwebs out, your subconscious is in control, and the trouble with that is the subconscious isn't the sharpest knife in the drawer. It can act, but it simply isn't capable of making a complex, shoot/don't shoot decision.
This is a case in which repetitive training can actually cause more harm than good. When you're awake and thinking, the conscious mind governs the muscle memory, but when you're half asleep, there is no governor reining in on the subconscious, and it's free to do what you've taught it, which is draw and shoot, without constraint.
As Col. Dave Grossman put it, "you've taught a puppy tricks". His theory is that the subconscious mind has about the same cognitive abilities as a dog. The question is, when your wife walks through your door, do you want that dog in charge of your weapon?
So what's the solution? How about setting the conditions so that the puppy can't access the weapon, but the master can? My way of doing that is to secure my weapon in such a way that it takes two, distinct actions requiring conscious thought to retrieve it. Specifically, I must open a closed drawer and draw the gun from a level III retention holster. I can still access the gun in a hurry if need be, but it's highly unlikely that I can do it without thinking, as in half asleep.
If any of you ever get the chance, I strongly recommend Col. Grossman's seminar on "The Bulletproof Mind". He addresses a lot of this in an interesting and entertaining way.