We have seen plenty of wildlife around WDW: deer, turkeys, bunnies, armadillos (alive!).
In fact if you take the monorail from T&T to Epcot (and back) right at dusk you will see plenty of deer.
As for being out at 3:00 am, while that is a bit odd, it is not out of the question. I didn't read the article but a couple of reasons-he was going to work, he was coming home from work, exercising before work, working, night owl, weirdo...
When you work at WDW, 3am is a normal time you'll be awake, and if it was EMH at MK, well, you're just getting out of the MK then. That's about right.
And WDW has tons of deer on property. You may think they are rare in FL, but because Disney is a giant nature preserve, deer are EVERYWHERE in WDW. This doesn't surprise me one bit. Though I'm glad he's okay.
Deer are getting out of hand pretty much everywhere on the eastern US, mostly due to hunting restrictions and habitat loss. They are getting pushed into WDW by the development around the property and they can flourish since corporate would never condone a "come hunt Bambi's kin weekend" at WDW. Worse, half the board would probably stroke out at the suggestion of shooting the female deer with contraceptives at the thought of the ultra conservative religious faction picketing with placards of "Bambi is a child not a choice" on the property. Best we can hope for is the board will authorize a couple hundred dollars for plastic deer whistles on the buses to minimize deer strikes on multi person (e.g. multi potential lawsuit) vehicles to cover their liability.
This could all have been prevented if the guy had a bike mounted taser....