This is a good idea. I have smoked tomatos and onions for a bbq sauce before but didn't think to try them on pizza. I've also smoked portobello mushrooms for a soup that my wife won first place with at the annual mushroom festival in kennett square pa. If you ever see the Mushroom festival on "All American Food Festival" on the food network, you'll see us.
Anyway, i have a weber smoker. Its electric and chincy but it works well. If you didn't have a smoker, you could always wrap some wood chips in some aluminum foil and toss it on the bottom of your grill. That works too. I usually cut my tomatos in half and place them on the cold side of the grill and keep the chips on the hot side. I gave my tomatos about 30 min. of heavy smoke. Carefull cause they tend to get soft and weepy, but they will have a great smoked flavor.