Is there a safety issue with freezing raw chicken with raw stuffing?
Your method of stuffing and freezing raw should be safe. Assuming you are following safe food handling and freezing methods, you will be fine.

Just prep your chicken and get it into the freezer within the recommended window of two hours that it can safely be in the "danger zone" of 40-140 F.

As it pertains to bacteria, you can think of freezing as stopping time. You are essentially putting all those pesky microbes on pause, so they can't multiply and have a big ol' botulism party on your chicken. So if your food is clean and safe when it goes into the freezer, it should be clean and safe when it comes out.

I can't see any point to par-cooking your chicken, and as James points out, it seems to complicate the process unnecessarily.

Also check out the USDA guide on Freezing and Food Safety.