Would it really? If you're doing genetic engineering already and you know what the genetic disorder is, it seems like you could then engineer a version of your DNA without the disorder and grow an organ from that.
I think if the new DNA kept the DNA encoding for the HLA markers there wouldn't be any rejection risk. HLA markers allow the immune system to tell which cells belong to your own body. When they do transplants, they check for HLA compatibility much as possible.
In my understanding, rejection is mostly due to things like cell surface proteins. It looks like cystic fibrosis is in fact a mutation in a surface protein, but at least it's only one. I'm guessing that's manageable...
