I am in pain after my pilates session this evening. Embarrassingly, my gut is too big for me to lie on my front without considerable discomfort. Then trying to to some of the exercises our instructor presents to us was excruciating. The worst bit was that she noticed that I was deliberately doing them "sideways on" as it were, and asked me why.
That doesn't sound good to me.
I'll assume it's your back that hurts.
The one thing that I'm told often is that if you even
feel it in your lower back, then you should stop!
The idea behind using pilates is to strengthen the core muscles which support the back, is to
not put strain on the back. It's the thing they seem to watch for more than anything else.
If your back hurts doing any exercise. You either can't do it, or you're doing it wrong and you need to stop!
Don't try and modify the exercises. The instructor should do that for you.
I think my instructor would blow a gasket if she read your post.