I only have a fairly basic grasp of physics and biology, and from what I know, the microwaves will heat up the water inside your cells.... Specifically the 2.45Ghz emitted by the magnetron in a microwave "oven". It will easily penetrate your flesh and heat you up from the inside out.... Like, on a cellular level. The water inside your cells can very easily and quickly boil, causing the cell to explode.... Especially when exposed to ~1000W of 2.45GHz EM energy. It's non-ionising so the effects will be limited by the amount of exposure, and limited exposure won't cause much damage. Your body will very easily heal, since you lose cells all the time. Prolonged exposure will kill you.

Also, activating a nearly 1kW magnetron in an open environment will have devistating effects on anything operating in the same frequency band, and likely anything on resonant frequencies, which will likely get you in trouble with the FCC (or local regulatory body), which can include aircraft, military operations, emergency services.... It's a long list. If they use radios as part of their normal operation, a powerful and unregulated transmission like this can basically jam their system making any legitimate broadcasts unintelligible. This can obviously put lives at risk.

With that said: do not do this.

I'm licensed to operate radio equipment in amateur radio bands up to 190W EIRP (if I recall correctly), and I don't think I've ever used anything more powerful than 50W, I don't own anything more powerful than 25W, and anything with the antenna attached to the radio (like a handheld radio) that I own doesn't exceed 10W, most are 5W. For me, if I was using anything over 50W, I'd want a band pass filter on my antenna feed line to eliminate spurious emissions on resonant frequencies just to be extra careful.

That all being said, since the damage from this guy has already been done, I wouldn't expect any further issues for him. I'm sure his biological systems have fully recovered from the exposure, and I don't expect it to resurface again. If it was higher frequency (ionising radiation) then he would probably already have died, and even if he didn't, he would be in for a lifetime of hurt, but yeah, 2.45Ghz is relatively safe by comparison.

Just to note, above x-rays are all the radioactive emissions that come from stuff like nuclear materials. Which is why they're called "radioactive" .... They're actively emitting radio (EM) waves. Usually well into the petahertz and exahertz, while ionising radiation starts in the very high terahertz range.

1Ehz = 1,000Phz = 1,000,000 Thz = 1,000,000,000 GHz (For clarity)