Increasing the distance between your atoms is not equivalent to killing you. Such an increase happens whenever you take a deep breath.
One could say that the totality of those atoms will cease to function as a biological, sentient computer. But this also happens every night, when our bodies switch into mental regeneration mode and are no longer under our control. Is a sleeping man alive? If yes, he is just as alive as grass.
By the way, one of ST:TNG episodes is entirely built around the idea that humans retain consciousness while in transport.
It reassembles an exact copy that, if it is alive, has no human soul and no intelligence.
If the copy is exact then nothing will be lost. If something is lost then the copy is not exact.
As matter of fact, most cells that human bodies are built with do not live forever. They have very short lifespan after which they are replaced with their copies.
In this aspect it is interesting that in ST:TNG transporters are used for transportation, but never for medical purposes. It would be very attractive to make changes in the pattern buffer before reconstituting the person. This would allow to heal *anything* in a second. ST:TNG stories carefully steer around long term storage of human patterns, but the issue did arise in a couple of episodes. It may be that the pattern is of holographic nature, where every bit is affected by all atoms and affects all atoms of the object - so it is computationally difficult to make targeted modifications.
Didn’t I read somewhere that no part of your body is more than 8 years old? In the time span, all of your living cells from that point in your life will have died and been replaced by new ones, in most cases many times over. Effectively, we ‘die’ and regenerate several times in a lifetime....
There is one episode of the New Generation where Dr. Crusher uses the transporter to cancel the effects of some sort of subspace illness that causes its victims to age quickly.
That's all I remember.
Star Trek started getting too silly near the end with all of the deus ex machina that were laying about to solve all of the problems in an instant: replicators, transporters, tachyon beams. Star Trek Voyager was especially keen on using tachyons to reverse time in order to cancel the effects of a disaster and get them out of impossible situations.
Curing all diseases by transporting a person with all of his parts but just minus the disease (e.g. cancer cells, etc.) would eliminate all of the drama.
Increasing the distance between your atoms is not equivalent to killing you.
But to actually argue this whole point is in the category of arguing about how many angels can dance on the head of a pin.