The 25-year-old McCarthy, a first-round pick in the 1999 draft, had two goals, four assists and 43 penalty minutes in 51 games for the Canucks this season.
Vancouver received a fourth-round pick in next year's draft from the Thrashers, who have won seven of nine to pull closer to Montreal in the race for the final playoff spot in the Eastern Conference.
Atlanta, which entered the league in 1999, has never reached the postseason.
McCarthy was drafted by the Chicago Blackhawks, who dealt him to Vancouver for a third-round pick before the start of this season. He has five goals and 17 assists in 185 career games.
Fata, acquired off waivers by Atlanta on Jan. 31, appeared in just six games for the Thrashers and recorded one assist.