If not putting undies on her makes her poo in the potty, I wouldn't put undies on her at home. I don't think it's cruel (though for us considering it's a fight to get undies onto my kids, I guess it's a little different, lol!)

Also wanted to say. Has anyone else ever commented on her behaviour? Maybe a teacher from preschool or someone else close to you?
BUT! If you feel that something might not be right, trust you instincts. You're her mother. You're with her 24/7. You know her like no other.