They evolved eating raw meat (and entrails!) Cats and dogs have a shorter, and I believe more acidic, digestive system than humans and they rarely have any effects at all from salmonella or ecoli, unless they are immuno-compromised. If you feed raw you have to be careful managing their waste as it is possible that it might be contaminated with those bugs, (like you would want to not be careful about handling poo.....) but many people feed raw and you don't hear about them being sick all of the time.
If it really worries you, you can put a whole chicken in boiling water for a short dip to kill the pathogens on the outside, but leave it for the most part raw - as far as I know that's where things like salmonella and ecoli live. That's why eating a rare steak is just fine, but hamburger is a bad idea- with the hamburg you've taken the outside and ground it all up putting it inside...
Now parasites are a different matter - cats and dogs can get stuff like giardia and it will affect them. I would guess that raw pork (because of trichinosis) probably should not be on the menu for either of them.

