Well, you are expecting an interaction with the microwaves used to heat the food
to now generate your externally sensed signal.
I agree. If all you're doing is monitoring the microwaves, you might
as well be monitoring "is the magnetron on". It will tell you nothing
about the temperature of the food, which is why people have been talking
about probes. I have used a pyrometer to measure the temp. of an object
in a chamber - this was bread in a vacuum cooler.
<story>
When you get the bread out of the oven, you can't slice it until it cools
some. For a bakery, this is very expensive, having bread just sit there on
a rack cooling, and not going out the door. I've seen a loaf of bread go
from about 250F to about 80F in about 30 seconds. You pump it down, the
water that was going to evaporate anyway evaporates, and sucks the heat
out of the bread as it does. The vacuum lowers the boiling point, you see.

</story>
But anyway, a pyrometer is another way to measure the food temp,
but that's only on the surface, which would be misleading anyway.
I'd go with the thermistor probe.
And about controlling - there's a microwave at my office that has a
"defrost" setting, and what it does is run for about 15 seconds,
and idle for about a minute, and run for about 15 seconds, and so
on, so you don't need any kind of fast switch, if you were thinking
of PWM control. I guess it's still PWM, just with a period of about
a minute or so.
Cheers!
Rich
Cheers!
Rich