Hey Fenrir...I think it's awesome that you went in and showed them how to do that! How cool!
You'd be surprised how many places are open to letting you show them the best way. Sometimes if you do the research and are willing to show them, the managers can be pretty receptive.
My experience is that most of these places are willing to do things the right way, particularly if you make it easy for them by telling them how to do it.
I have found that the best approach is to have them set up a gluten-free tray. That way all the employee has to do is pull out the tray, go over to the designated gluten-free work station and as long as they change gloves and use the utensils and ingridients on the tray it should be safe for celiacs. So basically they have this 2ftx2ft tray dedicated to gluten-free pizzas. The ingriedents are taken directly from the bag/container when first opened and put into containers on the gluten-free tray. Only the gluten-free meats are only the tray and I made them up a little list to keep that register so they can tell people which ingredients they can have on a celiac safe gluten-free pizza. More or less it is bacon, and pepperoni and most of the fruits/veggies.
This also happens to be the way Erberts & Gerbert's makes their subs.