According to the records kept by interpid weblog The Deadball Era, no fewer than three ballplayers have been shot and murdered by bartenders.

Here are no fewer than those three (each player listed with career WAR, click images to embiggen):

Frank Bell, -0.5 WAR (Profile)

From an unspecified paper on April 15, 1891:

Pat Hynes, -1.1 WAR (Profile)

From The Sporting Life of March 23, 1907:

Larry McLean, 6.6 WAR (Profile)

From the New York Times of March 25, 1921: