I think if you just cooked them in water, that would be fine. You won't have the onion anyway, and it's the only think I'd think would be different sauteed rather than boiled.
I generally don't put oil in my soups. I just "saute" the onions/carrots/celery (usually one of these, not all of them at once) in a little cooking spray and water. They take longer to cook, than they would if you were sauteeing them in oil, but they bother my stomach far less.