1) The cherem was applied against certain people practicing certain specific practices. a) Those people no longer exist (a cherem does not carry over to as of yet unborn children) and b) those specific practices are no longer practiced by anyone. (Even in the absence of point “b”, point “a” still applies and is sufficient on its own.)
2) The gedolei talmidim of the Gra recognized the error of the cherem in the first place and recognize it is inapplicable. This is evidenced by the fact that the spiritual heirs of the Gra today completely intermarry their children with Chasidim’s children, they learn in Chasidish yeshivos and accept Chasidish bochorim and yungerleit into their Litvish yeshivos, and sit and work with Chasidish Gedolim on Torah and communal matters on the Moetzes Gedolei HaTorah and other Torah bodies that are fully integrated with both Chasidish gedolim and Litvish gedolim who are followers of the Vilna Gaon.