I believe that the deep knee squat is one of those ‘contra-indicated exercises’ that needs to be viewed in a differential light. If I am on the floor and want to come up to a standing position, I usually do so from a deep knee squat. I have some older clients who want to maintain that ability, and I see nothing wrong with that.
However, if I had any amount of weight on my shoulders, I would think twice about it for myself, and I would advise others not to.
As LaRue pointed out, it depends on the individual circumstances.