Microwave-IR thermometer

The first question to answer is, "is there any point?". As microwaves cook food from the inside out, the temperature external to the food is hardly relevant.

Oh, come now PW. Microwaves penetrate any food item the same way as any other form of energy. So the old wives tale that it cooks from the inside out is not quite true. Microwave energy is absorbed by water molecules. If the outside of something is dryer than the inside, (such as a stale roll or biscuit) then it almost seems that it is cooking from the inside first. But that is an illusion. Water distribution is the key.

If you try to thaw something frozen, you will see what I mean.

To answer the question, it depends on the properties of the IR sensor. If the sensor is inside the oven, it is likely to become a conductor and absorb power from the microwave source. That may very well burn out the sensor. If it is looking through a hole(s) like the mfgs put in the little window, it may work. But those holes are sized so that the microwaves can't leak out. Note that IR sensors do not generally see through some types of plastic.