Dangar

Answer: Because only young John Connor is concerned about that, not the future John Connor that sent the terminator back. Future John Connor wants the terminator to do everything it can to protect his younger self.

lionhead

Answer: Older John Connor lives in a universe where most of humanity is dead but the survivors are all united against Skynet. He likely knew that humans in the past might even side against the Terminator, so he did not reprogram it not to kill, as saving his past self is priority. The T-1000 was also a human infiltrator so the T-800 had to get ready to kill something that looked human. Also, according to side canon the T-800 was sent back immediately after the T-1000 was sent as Tech Com finally defeated Skynet, so there might not have been time to fully reprogram the T-800 beyond its mission.