Puncturing the intestines makes the job of butchering even less pleasant, but you just clean it up. Surface of meat should be cooked high enough to kill any bacteria that might be on the meat. There will be NO bacteria inside the meat that has not had it's surface exposed to the air. (that is standard meat handling, any meat, any source)
There should not be much if anything inside the intestines of chickens you butcher at home, because if you are doing a proper job, you have withheld food and water to give the intestines an opportunity to empty out. If it is an emergency butcher, you will be happier if you are careful to not puncture the intestines, but you have not poisoned the meat if you do.
Also important: when you are butchering chickens, wash your hands before you put your hands into your mouth. The chances of getting any salmonella are pretty small and if you do, it will probably just be some intestinal inconvenience. But always go overboard with food safety.
