Here is my reasoning. The two rapists were most likely wanted criminals. They were going to kill Ned Beatty and Jon Voight and perhaps just leave them somewhere, knowing that it was likely someone would come looking for them sooner or later. They just figured they would vanish in the woods. They were not just standing there waiting for Beatty and Voight: how could they have known they would come ashore just there, or even that they were on the river (unless of course the hillbillies up the river told them)?
They must have been hunting, and if this is the case, then they must have only had one gun, or both would have been armed. And that gun was a shotgun–double barreled as I recall. That gun was buried with the dead man.
The man Jon Voight shot was armed with a standard rifle. He also had teeth. And the dead man in their party (was it Ed? I forget as this was a couple weeks ago, and not important enough to post until now) had no gun wounds, and that he passed out from nervous exhaustion was the most logical explanation.
And even while watching the movie climbing that cliff made no sense to me. If the guy had shot their guy, he was still pretty far up river. If he was heading to that cliff, it was going to take time. Burt Reynolds was hurt, and they were still, no matter what, going to need to get down river to get him help. The time to go was then, not to wait until the guy, if he was there, caught up with them. And even then, that was a long distance at which to hit a moving target, firing at that angle.
So my take is that the second criminal got away scot free, and the men managed to kill an innocent man, who was the hunter the sheriff was asking about.
This seems to be a minority opinion, although not absent on the internet. Again, it is complicated–no doubt somewhat intentionally–by the use of the same actor.
As to the rape, I really have nothing intelligent to say. Maybe I will tomorrow. This is a violent, sometimes very unpleasant world, but there is nothing deep in making that obvious point.