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.

I don't think the problem is the freezing per-se, it's the likelihood of ending up with things not fully cooked, or of them being in the danger zone (between 40 and 140 degrees Farenheit) for too long. If the total cumulative time in the danger zone for any part of the bird or stuffing is within 60 minutes (some people say 120 minutes, but that may include time while it's cooking), you should be fine. When you want to cook them, you'll have to defrost them thoroughly in the refrigerator (probably for at least a day or two) and make sure when you cook them that the coldest part (usually the centermost part, but not always) is up to the recommended 165 degrees Fahrenheit. If you were to try to cook them directly from frozen it's likely that the outside would be burned while the inside would still be cold, or you would have to cook them at such a low temperature that they would spend too long in the danger zone. If you were to thaw them on the counter, they would certainly be in the danger zone too long (every minute at room temperature is a minute in the danger zone).

I think half-cooking them would only increase the likelihood of safety issues due to multiple warming/cooling cycles.

Of course, as with most food safety issues, there's a good chance you will be fine anyway, but no reputable professional would risk going outside the FDA guidelines without a good reason and probably a warning to the consumer as well.

The FDA provides online Food Safety Information describing the risks. You can also call them with questions.

Fresh poultry is generally kept at "safe" chilled (below 40f), but not frozen temps for extended periods. Keep the chickens or Capone refrigerated until your ready to stuff the get them back in the fridge or freezer as soon as possible. You may even want to chill the stuffing before use.

The safety issues with stuffed poultry generally come when thawed and then cooked-reheated. The meat and stuffing may thaw at different rates. If they are not completely thawed in the fridge, you run into the issue of either the bird must be left at room temp too long or a very long defrost time. If the chicken or capon is cooked frozen or still partially frozen. You'll get uneven cooking. By the time the stuffing hits 165 f the bird will be dry.