This sounds almost exactly like what happened to me in my very first fort of the new version.
I ended up posting about it on the bug tracker:
Bug 0009344Based on that, I'm going to throw out a guess that what probably happened to you was that a random husked bird (or birds) flew onto your map covered in heinous murk, and it attacked either a dwarf or animal on the surface, transferring the murk covering to them and converting them into a husk. Then that victim attacked something else and spread it around, which in turn attacked something else, eventually culminating in the full zombie outbreak experience.
I never worked out whether the wildlife arrived on the map already infected or if it was somehow converted after arriving, but it was only ever birds, so it might be related to the bug where you can have embark locations that are good or neutral on the ground but evil a few z-levels up.
Of course I could be wrong and you could be dealing with an entirely different bug, but the end result sounds very similar to what I ended up dealing with.
I was really bitter about having to give up on that embark location, so I tried starting a second one in the same region, but that gave exactly the same results, so it affected the entire region. So yeah, making a new world is probably your best bet if you want to be sure to avoid it cropping up again…