There is not going to be an immediate and direct impact with the trials and the connection to Native Americans.  The trials were so domestic and inwardly driven, shaking Salem to its very foundation, that the relationship with Native Americans became a secondary issue for those living in Salem.  I do think that that there was an overall perception- based effect.  The primary issue in the Salem Witchcraft Trials was the fear that was rooted in "the other."  The idea of this "other," a fear of witches, gripped the town and became the root cause of the accusations.  The individuals who were initially accused were those perceived to be "different" in Salem.  This idea that "the other" was something to be feared and demonized undoubtedly would cast a pall upon any potential relationships between the Salemites and the Native Americans.  The former perceiving the latter as a form of "the other" would undoubtedly impact how perception was to be constructed as well as the need to dominate the other being present.  This would impact and affect relations with Native Americans based on the inward draw of fear and the lack of trust that would make collaboration with them impossible.