I might have known that somebody would email me this question:
'Can you kill bacteria in a microwave?'
Without bothering to do any research or carry out an experiment (what else would you expect from me?) I'd say 'yes'. The microwaves used are at the right frequency to make water molecules vibrate, all living things have water in them and don't like being heated up for long. As long as the oven has enough power, then after a while they will croak.
How long you need to keep bacteria in the machine, I couldn't tell you.