If your instructor knew about your injuries and still didn't give you an alternative exercise then they're bordering on negligent, and I suggest you find different class.
Most people come into pilates as a means of recovering from injury, or to cope with chronic physical impairment.
A good instructor would be able to give at least one alternative exercise sitting / standing / lying on your back etc, almost no matter what your injury.
She didn't know: its a mass participation free drop-in class at La Santa of about 50 people.