I had a long talk during open mat last week with a teammate who is also a trainer/strength coach/whatever. His question was one that I have heard bandied about quite a bit. Is the loss of lumbar spine curve at the bottom of the squat problematic? My response was: for whom, for what.
Why are we lifting? If the athlete wants to compete in a sport that requires squatting with a barbell then you've got to squat with a bar bell and to a certain depth. If the athlete does some other sport then we absolutely should not be squatting folks who cannot maintain lumbar posture. Folks participating in a sport more probably will be training outside the gym and will tend to push beyond the point of discomfort outside of your supervision as such they are more likely to be permanently injured. Generally speaking you can front squat them, or just eliminate squats all together. Would it be easier to get them monstrously strong with squats? Yes. Does that mean it is worth the cost:benefit analysis of the movement? Not in my opinion.
For the general fitness client things get a bit trickier. I have seen exactly zero general fitness clients walk in with proper mobility/stability to squat on day 1. However for these folks the fitness and aesthetic benefits of the squat are higher. We don't need to push the load (as would be required by an athlete seeking performance benefit), and can spend more time focusing on the movement. So I tend to (eventually) squat my general fitness clients more often than not. Even if it is simply including goblet squats into their warm-up.
As coaches we need to take a good hard look at what the client wants, needs, and how to get them there. Remembering that nothing prevents performance improvement like injury.