I think the machines vs. free weights boils down to "natural" movements, vs. "unnatural" movements. So barbell squats, deadlifts, chins are natural, something someone might do during the day. Leg curl, leg extension, preacher curls are examples of unnatural. Unnatural are more like to cause injury. The fact that free weights must be done in balance activates supporting muscles that machines don't.
I don't necessarily disagree with you (I don't know much about weightlifting), but this line of argument could be used as an argument against riding a bicycle ("pedaling" is not a natural movement).