The Death and disappearance of notable people like the towns sheriff would raise questions among his peers who knew him well, which in turn would lead to Hawking labs having to kill the other nosy cops. The sudden suspicious death of law enforcement and civilians in a small town where such occurrences are rare could lead to the possibility of the more powerful federal entities like the FBI stepping in to investigate.

It would be more efficient to discredit and destroy Hopper, by taking photos and footage of him in an unconscious OD state and use that to discredit him as a junkie.

I'd think Benny's death was as a result of Agent Connie Frazier being a murderous psycho than standard protocol. If killing was the norm Hopper and Joyce would have been shot on sight. Hooper would be dead twice over since he had been confronted by agents on the two occasions he snack onto the premises.