Is it wrong that I'm thinking of opting not to have children with my girlfriend that has heritable autoimmune disease?
How bad is the autoimmune disease she has?
The disease is very painful and the likelihood of having a healthy baby is small.
It's understandable to not want children under the circumstances. It's fine for people to remain childless or if you do want children there is always adoption. Adoption is a great choice to give a home to a child that needs one.
That's not helping, I'm still freaked out.
This is a complicated situation, especially if you already have a lot invested with your girlfriend. It would be best for you both to talk with a therapist about how you feel about having children moving forward.