Of course, there are many criticisms against the Smith machine, and they do have merit. However, Smith machines are only lacking when compared to perfection; in this case perfection would be using convential free weights during workouts, ie, dumbbells and barbells. Of course, dumbbells and barbells are better, but Smith machines are still beneficial.
Barbells and dumbbells recruit additional muscle when training, because you need to stabilize the motion by yourself. When you use a Smith machine, the machine stabilizes the motion for you throughout the entire range.
This makes it easier for you to perform the motion safely, but the problem is that you will not recruit muscle fibers used to stabilize the motion as you would using free weights. As a result, the level of development for both muscle mass and strength will be lower while using the Smith machine than while using free weights. But think about that - your workouts may lack in comparison to a workout using free weights, but that is not to say you will not gain both muscle mass and strength.
Sounds like you may not be unable/comfortable doing squats using a BB and a rack, which we all know is preferred, at this time due to physical issues.
Do what you can vs doing nothing IMO..