Fungus gnats, if already exist, can lay eggs in the soil and start the vicious cycle.  
However to minimize the infestation or delaying or stopping its its beginning, one can microwave the soil hoping that the Fungus gnats or other creatures eggs are destroyed.

If it makes sense, is there any negative consequence of heating the soil by microwavingg other than the stinking smell for a while?

I had stored a couple of bags of Fafard soil outside which got some small holes caused by weeds from inside and it is possible that tiny bugs could have laid eggs in it. Now I am microwaving this soil as I need for potting a rooted cuttings as a precaution.
 

you can Check an old post about soil sterilization where farmer use heat on black mulches to sterlise the soil before first planting to attack namtodes etc...

I also hear microwaving depletes food out of its minerals etc. as for soil i think it would be great. i would be cautious about microwaving the slow fertilizer cause it might release some chemicals to the microwave interior.

for the smell and contamination of the microwave itself- maybe its possible to heat it in a sealed plastic container suitable for microwave use.

I think you'd be better off heating the soil in the oven. But I don't know what temperature would be suitable. I'd think anything above boiling point of water should kill insect eggs.

I wonder why your soil is stinking after microwaving?  Does it stink prior to going in?  I ask because I microwave potting mix when required for indoor plants and there are no odors at all.  

Visceral
"Using the word 'stinking' was a little harsh but I meant 'not a normal smell' spread in the vacinity. Many soil mixes do give out odor when heated. Un-heated soil may smell if one tries to smell it at close range.

Gotcha.  Well, I've had no negative consequences at all.  I use tupperware type containers, but I've read others use plastic bags.  

Hi Ottawanz5,
Take some meat and put it in the microwave oven :
Under 1 minute, the meat will get cooked. Humm. Insects are meat . Not in my cookbooks, but technically, they are !
After 2 minutes (or 5 - I don't remember how much it took to burn the meat the last time I "experimented") you'll get meat-coal.
Getting to the coal state, you'll get a "burn" smell.
Of course getting to the coal state, you'll have destroyed some nutrients and changed the properties of your potting-mix.

So for me, 30 seconds of microwaving should be fine - perhaps even 20 seconds .
I'm speaking for a flat layer of 1cm or 1/3'' .
Remember that the mix needs to have water. Microwave work on the water or humidity inside the mix or meat.

I had a bag of Fafard soil mix which was well moist. I put about 2 liters in a plastic bag and placed it on microwave plate that became about 2" thick layer of soilmix. I heated it for 4 minutes. When I spread it in a shallow container and churned it with a spatula I noticed a limped nematode in it. It was limped (most probably dead) but from the look of it did not cooked or burned. 
I know nematodes have many species and some are beneficial and can take care of grubs in the lawn. My new question is as to what possible damage nematode can do to a rooted cutting in such a soil if any left alive. I hope that it is beneficial type, if any are there in the soil and will lunch on fungus gnats eggs. I still have two bags of Fafard soil left.

I have microwaved my HP Pro Mix in the past.  I dampened it first, placed in a slightly opened zip lock bag and nuked for 2-3 minutes.  Never got a bad smell.

2-3 minutes in a closed zip lock freezer bag should do it. You could check the temp of the bag and not open until it cools. I think about 160 should do it. I believe you want to stay under 180 to prevent any adverse affects to the soil. Might want to Google to verify the temps.

I'm thinking wrapping in tin foil and throwing onto a campfire or something.smell won't be a problem and nothing is really going to survive.

Nothing wrong with microwaving the soil. I've done it.