Well, for one, the trainers that told you to squat on the smith machine should be castrated. As for your program, just switch over to conventional barbell squats instead of smith machine ones and continue on. Just make sure you get the movement mastered before you start adding the big weight to the bar.
The smith machine won’t kill you in the beginning, because you likely weren’t using enough weight to really hurt yourself. However, if you tried to do any sort of weight on there (shit, anything over 200 can’t be good I’d imagine), you probably would put yourself at risk.
Just to let you know. The two main reason the Smith is use less fopr squats and really most ALL exercise is
it makes you not use your stabilizing musculature to balance etc. you will get a HELL of a lot more bang for the buck out of Real squats they will hit your Whole body. Not to often in real life that the load you lift will be running on rail you know.
the smith forces you to follow an unnatural path. This Can be BAD!!!Puts Major stress where it should NEVER be Where as a real squat when done right you will move in a natural range of motion. Using all your musles etc.
In short its harder to real squat but safer and more effective even at a lower load.
Just drop the load do real squats. Live and learn.