Yes a crime was committed once but several crimes can be assessed from the same action.
No. Several charges can be assessed, but only one crime. Traditionally, this has meant one trial. I am aware that this is not unique, except perhaps in the amount of time that has elapsed between the crime and the death. These types of things happen periodically, but that doesn't make it right.
In the case you cite, the parents beat the child nearly to death. They were tried and sentenced for it. If the child died a month, a year, or four decades later is immaterial to the crime committed. They condemned the child to a death sentence when they beat it, just as Mr. Barnes sentenced the rookie police officer to death when he shot him. If medical science had been able to commute either or both of those death sentences, so much the better, but the crime was committed and punishment meted in both, the long-term effects notwithstanding.
We have reached a point in society where we believe that someone has to be punished everytime something bad happens. I believe this thinking is symptomatic of that. You cite the helicopter collisions. I am well aware that the law has allowed for the punishment of offenders for crimes not directly related to their own if prosecutors can simply draw some connection between the two. Again, that doesn't make it right and, in a way, it absolves the real responsible parties - the pilots - by passing the blame onto a third party.
Locally, we had an incident in which a police officer was killed speeding in response to a report of a crime. Even though he was miles away from the crime at the time of his wreck, the criminals were charged with manslaughter in the case of his death. They had never met the officer, seen the officer, he never arrived at the crime scene, and he drove in an unsafe manner in his haste to reach the crime scene, resulting in his death. His death was sad, yes. It was tragic, yes. It was preventable, yes. It was the responsibility of the criminals, no. Again, however, something bad happened and someone had to pay. It's sort of the criminal justice equivalent of 'deep pockets'.
How far back do we go with such crimes? How much punishment is enough?