I am replying to the original title of the OP before the edit by David Z:
Is it possible to kill someone with a single atom and a particle accelerator?
The answer is no, and there is experimental evidence in the case of Anatoli Burgoski that you mention:
Bugorski survived longer than just a few days. In fact, the dude is alive and pretty well in 2018 at 75 years old. The accelerator incident didn't leave him entirely unscathed, however; he's human, after all. The beam burned a path through his skull and brain tissue, and, for the next couple of days after the event, the spots on his head where the beam entered and exited experienced some skin peeling. Bugorski lost the hearing in his left ear and now experiences constant tinnitus. The left side of Bugorski's face gradually became paralyzed, making it look oddly frozen in time. (Who needs Botox?) He has also suffered at least six tonic-clonic (aka grand mal) seizures and also experiences absence (aka petit mal) seizures.
You are asking about one high energy particle being able to kill.
The intensity of the proton beam that passed through Anatoli's head was $10^{13}$ protons per pulse. The energy of each proton 76 GeV, and he is still alive.
One particle is trivial compared to $10^{13}$ and, as another answer states we are all bombarded with high energy cosmics during our life.
The reason is that a charged particle will have a path with small interactions through matter, as discussed in other answers. Here is a bubble chamber picture of protons in a beam ( the number of protons in the beam is reduced for bubble chamber beams, for clarity in the pictures)

This worksheet is based on images recorded by the 2 m bubble chamber at CERN on 10 August 1972. The bubble chamber was exposed to a beam of protons from CERN ’ s proton synchrotron PS with a momentum of 24 GeV/c.
The electromagnetic interactions are those that generate the ionisation of the tracks, the width is less than a micron. Passing through the head the disturbance is minimal , similar to what is seen in the picture above. More damage happens with strong interactions, but those have to hit a nucleus, where two of the five protons entering have managed to do in the two meter chamber. ( the picture was picked because there was an interaction, the real probability has to count all the empty of interactions frames) . These strong interactions are the ones that can destroy cells by cascading through living matter.
The higher the energy of a particle the smaller the deBroglie wavelength

so the probability of hitting anything on its path is smaller with higher energy, a particle has to hit head on a nucleus which has dimensions of a fermi, for a strong interaction to happen.
Thus the answer is no, a single particle no matter of how high the energy it carries is, cannot kill. As we deal with quantum mechanics the correct framing is : "the probability of a very high energy particle to kill a human is infinitesimally small"
Now on some statements in your question:
but a much heavier object, like a gold atom, not a proton. (oh my god particle has roughly the energy of a baseball, 5 OZ at 94 mph, so an atomic mass of 197 means equivalent energy of a 61 lb object traveling at 94 mph - more than enough to knock an average person off their feet pretty easily.
An atom as it enters a body will immediately shed its electrons with electromagnetic interactions and will just be like 197 protons out of the $10^{13}$ in the beam hitting Anatoli's head. There is a probability that some of those $10^{13}$ protons have hit and interacted with the strong interaction, as in the picture above, in the head. What happens as far as interactions go, the end products will leave just ionizing, no cascade, as there is no cascade in the picture above. The velocity near light velocity means in a very small interval of time the particles near velocity c traverse the head and are out.
For a high momentum beam particle to transfer its energy to the body , the body should act as a rigid body. Instead it is a quantum mechanical system held together by electromagnetic interactions. A nucleus in the body hit and interacting directly with the projectile cannot transfer any momentum to the body, as far as the strong interactions go it is as if it is free, everything happens much faster than the electromagnetic bonds keeping the body in shape can respond to. The hit nucleus will react as the interactions in the picture, generating secondary particles which again will have a small probability of interacting strongly before they leave the head volume.
Shooting them from a distance where the atom would interact
It would interact as the tracks in the picture, just ionisation, and keep its course. The probability of a strong interaction with air is very very small.
The beam entering the bubble chamber in the picture above, was sent through air, because it was so few protons at a time, and when we had a glitch in picture taking we would joke that the cat crossed the beam!