I didn't vaccinate my first set of chicks because the hatcheries said it wasn't necessary for a small flock (read: economically feasible for a small flock). I spent months researching everything, designing and building a coop, the usual routine. I ordered 30 day-old EE chicks from a small breeder and they seemed really healthy. I was excited and got pretty attached to them.
As they started to grow up, I started losing birds and found out they had Mareks. I don't know if they were already infected with it, or if they got it from the apparently healthy chickens living across the street (in the same air stream). At the time I figured well, that sucks, I'll have to lose some and keep the strongest ones and end up with a resistant flock. I'll have birds that are well suited to the particular conditions on my little farm and everything will be fine.
Unfortunately it was a pretty virulent strain.
Only 3 birds survived.
Do I vaccinate now? You betcha. Is vaccination necessarily unnatural or unhealthy? No. When I vaccinate my chicks for Mareks I am exposing their immune systems to a naturally occurring variant of the Mareks virus (there are several strains; some are harmless to chickens, some cause a milder disease, some are fast and deadly). Their little immune systems quite naturally mount a response to it so that when the virulent strain comes along they are able to fight it off fast enough. Nothing unnatural about that, unless it's unnatural to give them a fighting chance.
I vaccinate my horses, my dog and my cat. I've seen other (unvaccinated) animals suffering with easily preventable diseases. I myself am effectively immune to things like polio and pertussis. Smallpox is no longer the scourge it once was. Our immune systems are unable to withstand rabies, but if I get bitten by a rabid animal, there are vaccinations available that will save me from a horrible death.
And I just gotta say, on the subject of science, I like living in a comfy house, having a hot shower, using a computer, driving a car, traveling by air, talking on the phone, etc. I like knowing that if I suffer a terrible injury or medical emergency, there's all kinds of specialized help available to me. I got nothin' against science.