Watson does not say that Helen Stoner was killed. He says that she recently suffered an "untimely death."
The events in question occurred in the early days of my association with Holmes, when we were sharing rooms as bachelors in Baker Street. It is possible that I might have placed them upon record before, but a promise of secrecy was made at the time, from which I have only been freed during the last month by the untimely death of the lady to whom the pledge was given.
Helen is the lady to whom the pledge was given. She wanted to protect the ancient family name of Roylott. It was concluded that Dr. Roylott had been accidentally bitten while studying a poisonous snake. It is quite possible that Heelen died of an illness or even that she died in childbirth. It seems likely that if she had been murdered, Watson would have said so. But there is no reason to suppose that she was killed. She was engaged to be married, and she inherited all her mother's assets after her stepfather was killed by his own snake. Holmes told Watson that the total income from investments was about eleven thousand pounds a year, so she and her husband would be wealthy. Nothing was said in the story about what was done with the property at Stoke Moran. No doubt Helen disposed of it because of all the bad memories attached to it.
Watson says in his introduction that the events in the story took place in April of 1883. The story was first published in February of 1892. So Helen was only about thirty-nine years old when she died. This was indeed an untimely death, but it does not sound like a murder.