Gotta side with Mrs. Scot on this one:
In general, mixing raw and cooked meats is a big no, no. Recently Chef Robert Irvin on a recent episode of Restaurant Impossible blew a gasket when the restaurant owner he was evaluating made a pizza using raw hamburger. He ripped the owner a new one on camera then stormed through the dining room pulling pizzas off of diners' tables and throwing them in the garbage.
I'll admit that I have used raw sausage successfully on top of my pizzas in the past. I don't engage in this practice anymore, however.
When we open our restaurant, I plan to have make-tables fully visible to the public and using raw meat would create a PR nightmare--Lucy, you've got some 'splaining to do! Cross contamination would have to be carefully watched--it's preferrable to have a refrigerated prep table where the ingredients are not inherently toxic if mishandled. Using raw pork on top of a pizza would also violate widely held best-practices of many culinary schools, as well. This practice is just not professional, in my opinion.
Weighing the risks vs rewards, I have switched to lightly browning all sausage and bacon before adding it to the pizza in our experimental kitchen. While using raw sausage on a pizza might be OK in the privacy of one's home if handled and baked correctly, if the chef is really careful, I don't think its a good idea in a commercial environment. Public complaints, health department questions or citations, and possible contamination with lethal bacteria, all equals a great deal of potential trouble. And for what? Extra oil and some additional flavor on the few pizzas that utilize uncooked pork. Not a good gamble.
