SCD yogurt has a large amount of probiotics in it, and people's bodies have to adjust to it slowly. Try eating just a teaspoon (or even half a teaspoon), and see if that goes over okay. Two ways that can help you tell if it's the milk protein or the probiotics that bother you are to freeze or cook the yogurt. The heat/cold will kill most of the probiotics. If you still react to it, then you know it's the milk protein that is the problem.
Also, if cow yogurt is a problem, you can try goat yogurt. Generally, people with a cow problem can handle goat. I've personally never tried it, but the popular opinion at the yahoo group is that raw goat milk makes a much better yogurt than pasteurized goat milk. A lot of people say the pasteurized tastes kind of funny. If the goat doesn't work out, you can try making yogurt from almond milk or coconut milk. A more difficult process, but it can be done. If all that fails, you may just have to take an acidophlius supplement instead.
And not to derail your thread, but I just wanted to share that my seasonal allergies are a gazillion times better since starting SCD (since 12/01/08). I don't know if it's the diet, or the raw local honey I eat everyday, but I haven't started itching yet, and there's a ton of stuff in bloom (I live in Arizona).