The leaves of tomato plants don't become toxic until around the time they have fruit. I think it's when the fruit starts to ripen. So, eating young plants won't hurt them.
You could get a roll of wire and fence the tomatoes off from the chickens. Otherwise, I don't think you're going to get any tomatoes. You can also try growing other things for the chickens to eat. They really crave green feed. If they don't have enough grasses and dark leafy greens in their diet, they'll eat whatever is in the run. Letting them free range for at least part of the day, if your yard is not too risky, also takes some of the pressure off plants in the run.