Anything that breaks down due to heat is going to break down no matter HOW you cook it. Boiling only "destroys" nutrients by leaching them away into the water, which is the same reason that other people say that steaming/microwaving is better.
Thiamine, for example, is highly water soluble, so boiling is out. But it also breaks down at 100C, so you can't really cook it either. Niacin, on the other hand, leeches into water, but it's not heat-sensitive, so you can cook the hell out of it, as long as you don't get it wet. Folate is so fragile you can't leave your leafy greens in the sun without it breaking down (common with acids).
Basically, almost everything is better uncooked, but a lot of things are impossible to eat if you don't cook them enough to break down the cellulose. So eat a balanced diet, and stop worrying about the microwave.
First of all, it is extremely rare for the yolk of an egg to become contaminated if the egg is reasonably fresh. Contamination only tends to occur when the egg is quite old and the yolk membrane weakens. (Source)
Now, that said, egg yolks begin to set at a temperature of 62° C (144° F), and salmonella can be killed at temperatures as low as 59° C (138° F), so it actually is possible to "cook" the yolk sufficiently to kill any bacteria without letting it set, but you have a very small window to work with, so you need to be careful. If the temperature is even 1° too low, you'll just be encouraging the spread of more bacteria, and if it's even 1° too high, you'll ruin your recipe because the yolk will set.
Nevertheless, if you have a reliable, uniform heat source, you could attempt to heat the egg to 60-61° C for about 1 minute.
Unfortunately, you won't be able to use the technique used in other recipes - such as Bavarian cream - of simply using the residual heat of the other wet ingredients to cook the yolk sufficiently for safety while not allowing sufficient time to set. Dark chocolate is the most heat-resistant but will easily burn at temperatures significantly above 50° C (125° F). Mixing the chocolate with cream may raise this temperature slightly, and I admit to not being certain of the exact amount, but I'm pretty sure it won't get you up to the required 59° C - and it really actually needs to be much higher than that because the temperature must stay that high for several seconds after adding the eggs.
So my advice to you is to either:
- Pre-cook the yolks very carefully to a temperature just below 62° C (use a thermometer!); or
- Use very fresh eggs from a reliable source; or
- Don't eat mousse made with egg yolks, if you can't tolerate the (very low) risk.
Best Answer
Microwaves do not kill bacteria, heat kills bacteria. The higher the temperature, the faster those bacteria will die off.
"Instant death" for most bacteria (including salmonella) is about 160° F (71° C). You only need a few seconds at this temperature. The notoriously strict USDA recommends 160° F for egg dishes but is considerably more lax about whole eggs and just says to cook until firm. Very few eggs are contaminated in the whites or yolks, so the risk is very low.
Pasteurization begins around 57° C (135° F), so many bacteria are killed before the egg coagulates (at 63° C / 145° F), which is why the USDA is not very strict about it; if an egg by itself is "firm" then it's generally already been hot enough for long enough to ensure safety.
Unfortunately, microwaves tend to heat (a) quickly and (b) unevenly, so if you are concerned about food safety and insist on making eggs in the microwave (not recommended), be sure to use short bursts and stir several times, otherwise you might end up with a combination of uncooked and overcooked parts, which is bad for food safety and for general taste and texture.
Note that there is not only a possibility but actually a certainty that some salmonella is still there, assuming that there was any to begin with. Cooking is equivalent to pasteurization and that does not kill every single bacterium, nor is it meant to; it just kills about 99.9999% of them which makes the cooked item safe enough to consume.