I recently bought some frozen pizza from Lou Malnatti’s. They recommend thawing the pizza in the refrigerator. Why can’t it be thawed on the counter, at room temperature? If the issue is bacteria growth, wouldn’t the high cooking temperature of the oven when the pizza is being heated destroy the bacteria anyhow?
Yes, but such cooking will not necessarily destroy the toxins that the bacteria have produced. You can cook botulism-infected food until it’s blackened Cajun style, but you’ll still get sick. So, yes, it’s a food-safety issue.
WAG: Cooking won’t kill them all. By starting it’s defrosted life in a fridge you start cooking with less bacteria so it’s less likely to spoil or poison you. Even if an oven goes to 220 degrees C parts of the food won’t until all the water has boiled away. Those parts won’t go above 100 degrees C.
The safest way to defrost is in the microwave, second is the fridge and third is at room temperature. This is strictly due to bacterial growth.
Leaving frozen food to defrost on the counter is usually OK as long as you don’t let is sit out too long or let the surface of the food get to room temperature while the core stays frozen (by putting it in the Sun, or if the cut of meat is very thick). To prevent irresponsible countertop defrosters from getting sick, it is always recommended to defrost in the fridge.
To emphasize a point solkoe made, the advice to defrost in the fridge is not specific to a particular pizza brand, nor to frozen pizzas in general. It applies to any/all frozen food.
Whether any given manufacturer of package food puts that instruction on their label has more to do with their legal department than their culinary department.
actually the toxins are quite sensitive. Ten minutes at 100 C will certainly destroy them (e.g. the toxins use for facial injections must be stored on ice). It is the bacterial spores that survive cooking - however the bacterial spores are usually only dangerous to children
http://www.fda.gov/fdac/features/095_bot.html
One question that perhaps someone can enlighten me on. the toxins are proteins - so how do they not get digested and boken down by the gastrointestinine system- and how do they get across the GI walls into the blood stream?
That is only true for certain toxins, such as the botulism toxin you mentioned. It is NOT true for all of them. Cite:
So why would you defrost the pizza in the first place? What’s wrong with just putting it straight into a hot oven?
some food is recommended as being cooked from frozen. I think it is to ensure an proper cook, e.g. to stop some things being burnt in parts and frozen in the the other
That looks like some damn good pizza, shiv! 
That part may indeed be brand specific. Lou Malnati’s is famous for their deep dish pizza - it’s a good inch thick of dense cheese. If you cooked it from frozen, the middle would be cold goo when the outer crust was turning to charcoal.
Maybe this is a dumb question, but if heat won’t kill 'em, then how is it going to be safer to eat your pizza (or whatever) after being cooked than if you let it thaw and ate it at room temp?
I’m feeling real dumb at the moment. I have never paid this much attention to thawing methods in my life. Is this all something special about meats (I’m a vegetarian), or do I need to shape up my ways to avoid dying a nasty food-related death?
Any food will begin to thaw at any temperature above freezing. It can thaw at 33 degrees, 35 degrees or 70 degrees (most fridges are set around 35 degrees). Bacteria, on the other hand, tend to grow really well at 40 degrees and fairly poorly at temps below that. So if you keep the food above freezing but below 40 degrees, it’s in “the safe zone” for reducing bacteria growth while defrosting.
If you defrost it at 70 degrees, or room temperature, it’ll be faster, sure, but it’s also in the “danger zone” for bacterial growth. Even heating it to cooking temperatures will not kill all the bacteria, and will not render all bacteria-emited toxins safe to eat. Since there’s more bacteria when you start, you increase the chances of something surviving. And toxins will make a person just as sick as some bacteria.
Interestingly, the fastest way to cool something solid like a steak is not on the counter - it’s under cold running water. This keeps it in the “safe zone”, and the water is a better conductor of heat than air is - so it conducts heat to the food faster than air does. I don’t think this is all that practical for a pizza, however. 
Vegetables and fruits can cause problems, too. People have gotten food poisoning from foods like melons. It’s suggested you wash them thoroughly before cutting them.
You also are best to put any cut or cooked foods - even vegetables - away in the fridge promptly.
Food poisoning from vegetables typically occurs from improper food handling (contamination) rather then time/temperature abuse, although it is certainly possible for vegetables to spoil and harbor bacterial growth.
Thawing techniques vary in safety because of the time it takes to thaw at a given temperature, not just the time or temperature alone. Counter top thawing is very slow at a high temp. Refrigerated thawing is even slower, but at a much lower temp. Thawing under water is extremely fast at a temp just lower then room temp, because of the conduction of heat through the water, and the convection of water flowing over the food. Microwave thawing is also fast, but is not recommended unless the food will be cooked immediately. This is because the microwave will heat the food unevenly and will raise some parts of the food well into the temperature danger zone. If the food is fully cooked right away the bacteria will die before having a chance to reproduce.
Cooling food is much more dangerous then thawing it, and in my opinion, causes a lot of needless food bourne illness. How many times have you taken home left overs from a restaurant in a closed container and placed it in your fridge without opening it? The food was in the temp danger zone from the time it was placed into the to-go box until several hours after you poped it into the fridge.
Cooked food has already had most of its bacteria destroyed in the cooking process. You are starting with a much lower number of bacteria than uncooked food. In theory, a well cooked lasagna, for example, is sterile. If you kept it in a closed container it would never rot. Most likely, your cooked food is not sterile because it hasn’t been cooked long enough and its been sitting on your plate for an hour or so.
Either way, the cooking gives you a bit larger window of time before you have to put it in the fridge.
One of the extra features in the movie SuperSize Me showed the host comparing MacDonald’s french fries to chip wagon french fries. He let them sit in a closed container for several days. The result was the the chip wagon fries had turned green with mold while the MacDonald’s fries still looked fresh. His claim was that the MacDonald’s fries were fabricated in some way that destroyed its ability to decompose. In reality, they were probably cooked and stored a heck of a lot better such that they contained zero bacteria after cooking.