Of all the dangerous devices to disassemble, they're one of the safest. A phone charger might still have 400V across one of the capacitors ten minutes after unplugging it (if you're in a 230V RMS country, so have more than 400V peak-to-peak), but a microwave's high-voltage section is only powered when it's plugged in, and microwaves are so long wavelength that even if you reassemble the waveguide or outer case badly and leave gaps, there probably won't be dangerous levels of microwaves escaping as gaps much smaller than the wavelength in question don't compromise the Faraday cage.

if the diagram's any good, it should show the wave stirrer in the roof rather than on the ceiling of the food chamber. There's typically a waveguide to take the microwaves from the magnetron to the top of the chamber, then the wave stirrer is at the end of the waveguide to vary the angle that microwaves enter the chamber at. There's usually something to stop food splashing/spraying into that section, though, e.g. an extra few centimetres of waveguide afterwards with a bend in it.