He killed the humans because they were supposed to continue the spacejokey legacy of genetic engineering. Instead humans (as represented by Weyland) attempt to stop the process with themselves as a "pinnacle" According to the spacejokeys, humans choose to be a dead end within the genetic engineering legacy.
Humans created artificial intelligence instead of remaking themselves (and by extension the spacejokeys due to their shared DNA). This is why he started killing people when he examined David and heard of Weylands motivations for immortality.
The spacejokeys believe in self-destruction resulting in self-overcoming and the humans desire to cling to life and create artificial beings rather than remake themselves is an abomination from their point of view. As well as an insult.
why do people make the same threads over and over again on /tv/ ?