Thompson walked off the court just prior to the opening tipoff to protest a new NCAA rule on scholarships. He left the team to assistant coach Jim Riley, who watched the Hoyas, 12-1 overall and 2-1 in the Big East, jump out to a 24-7 lead en route to building a 50-31 cushion at halftime.
Georgetown, 12-1 overall and 2-1 in the Big East, led by as many as 32 points in the second half. Dwayne Bryant led the Hoyas with 16 points and freshman Alonzo Mourning, the nation's leading shot blocker, stopped nine attempts, including seven in the first half.
Dana Barros led Boston College, 8-5 and 1-2, with 16 points. The Eagles have never won at the Capital Centre in eight tries.
Thompson, following up on a promise he made Friday, never saw a point of the rout. He left the arena in a waiting car after slowly walking past the media, refusing comment.
The 1988 U.S. Olympic coach left the game to protest Proposal 42, an NCAA rule approved Wednesday that will create more stringent entrance requirements for incoming freshmen.