At the Cyberdyne building, the T-1000 drove through a window in the building in order to commandeer the police helicopter. After entering the helicopter he ordered the pilot to "get out" -- which the pilot did -- instead of killing him:
The helicopter doesn't have much altitude so the pilot might have survived the jump; the pilot obviously thought he had a better chance of survival by jumping than remaining in the helicopter with the T-1000 (and the pilot didn't even know the T-1000 was a Terminator or what a Terminator is).
Since it's possible the pilot survived yet it would have been easy for the T-1000 to kill him (e.g. by forming a blade and stabbing him), why didn't the T-1000 simply kill the pilot?
As a Terminator it's not like the T-1000 would have any moral qualms about killing him, and there's been such an extensive firefight already that investigators wouldn't be particularly surprised upon finding the pilot's corpse. On the other hand, if the pilot survived the jump he could tell a tale about a strange "policeman" who could turn into liquid metal -- possibly compromising Skynet's future. (Granted, it's doubtful anyone would believe the pilot and he'd probably be sent to an insane asylum like Sarah, but why take a chance?)
Note: I am looking for an in-universe answer.