I feed raw and just use common sense when feeding my boy as I do when prepping raw meat for my family. I do not brush his teeth or wipe his face/mouth after he eats. He's a pretty neat eater and always licks his mouth after eating to remove anything that's there. I don't like to be kissed/licked by him so I don't worry about that. He also doesn't go around licking stuff in the house. I do understand your concern and think it's great you are posing these questions.
If you can feed a balanced raw diet I think it's worth a try.
Can you post a picture of your boys belly/groin area? Have you absolutely ruled out fleas? Does he lick that area constantly?