It seems that the man who shot Ross was a Canadian man named Peche, Peshe, or Péché, (depending on the source) and was one of Pond's men. That, combined with the known antipathy between the two men was enough for Pond to be charged with murder.
The fact that he was subsequently acquitted at trial shows that, on this occasion, it was not sufficient to secure a conviction.
The paper Peter Pond: Map Maker of the Northwest (1740-1807), by Gloria Fedirchuk on the University of Calgary website includes the observation:
Fidler (Hudson’s Bay Company Archives E.3/1) indicates that Peche, one of Pond’s men, shot Ross under order from Pond. Pond was again tried and acquitted of murder
The Fidler mentioned above was Hudson Bay Company surveyor, Peter Fidler. In the article on Peter Pond in the Canadian National Biography it states that Fidler apparently wrote in his diary:
“Mr. Ross was shot by one Peshe, a Canadian, by order of Pond.”
It further notes that Péché:
"... afterwards traded from Slave River among the Chipewyans."