Whether it was under the English statute or the Massachusetts statute wouldn’t have made a difference to the issue of a pardon.
Under British colonial law, settlers were considered to have brought English law with them, as part of their birthright as true-born Englishmen. The English statutes were considered to be part of the statute law of the colony, which were then administered through the colonial courts. It’s called the doctrine of the reception of English law. It’s still part of the law of many Commonwealth countries, such as Canada.
For example, Louis Riel was tried and convicted of treason in Regina, North-West Territories, in 1885. The statute under which he was charged was the English Treason Act, 25 Edw. III St. 5 c. 2 (1351). That statute had been received as part of the law of the North-West Territories, and was administered through the court of the stipendiary magistrate who conducted the trial.
So even if the alleged witches were tried under the English act against witchcraft, that English Act would have been considered part of the law of the colony of Massachusetts, administered through the Massachusetts colonial courts.
The pardon power was similarly decentralised by the Imperial government. The document setting up a colony often contained some sort of delegation of the royal prerogative of mercy to the local governor, although there was considerable variation in the actual mechanics of this delegation, depending on the nature of the colony (Crown colony, mercantile plantation, etc.). If the Massachussetts governor at the time of the trial had the legal power to pardon, then I would assume that power would have been passed on by the revolution to the successor republican government of Massachussetts.
Again using the example of Riel, upon his conviction under the Treason Act, 1351, there was an application to the federal government to pardon him. The application went to the federal Cabinet because the Governor-General of Canada exercises the Crown’s prerogative power of pardoning for criminal offences committed in Canada, on the advice of the federal Cabinet.
To put it another way, the power to pardon is always considered to be one aspect of sovereignty. If the OP is correct and only Queen Elizabeth can issue a pardon for the Salem offences, it would mean that the British Crown still retains some limited sovereignty over Massachusetts - I don’t think John or Sam Adams would approve.