Microwave can kill bacteria directly. However, all bacteria are not the same. Some are fastidious and easily destroyed while other are quite stubborn, requiring special conditions of heat, chemicals etc to be killed. That said, I would like to think that both conditions ie. the heat and the microwave play synergistic role in killing bacteria.
The main killing effect of microwaves on microorganisms is undoubtedly because of the heat generated in the food and liquid by the microwaves, but there is a lingering debate whether there may be some 'microwave effects' on killing microorganisms.
Heat is generated by moving the water molecules in the microwave. The water in the cell is likewise expressed. Since the water inside the bacterial cell will be heated, the bacteria will die with the effect of this heat.