Unless you are using an oversized microwave (like industrial or scientific size) and a large protective shield for the camera, I doubt it would be practical to film the inside of a microwave oven while it is running, without destroying said camera.
If you are only looking to simulate the effect, you may disconnect the magnetron circuitry from the microwave oven. First off, discharge the high voltage capacitor. In most ovens, you will find a circuit board with a relay, with two wires leading to the primary winding of a heavy transformer; the secondary winding leads to the magnetron. You should be able to simply disconnect the primary side of the transformer, from the circuit board (preferably) or from the transformer itself. Avoid touching the secondary side as it is connected to a high voltage capacitor even if you have already discharged it (you might still get a very bad shock from a partial discharge).
Depending on the complexity of your oven it might or might not work (I suppose some microwave ovens would detect this as a fault). If you want to also record the classic magnetron hum sound, do it in a separate track, from outside, before disconnecting the magnetron.
Serious warning / disclaimer:
Messing with microwave ovens (and any other electrical appliance) can be dangerous! Attempt to do this only if you know what you are doing. In any doubt, ask an experienced electrician or electronics professional friend for help.