Remember Occam's Razor - the most simple explanation is the most likely. ("among competing hypotheses, the one with the fewest assumptions should be selected.")
Pilot or co-pilot goes all jihadi, wrestles with other pilot for control on the aircraft (wild flight maneuvering), sane pilot or air marshal shoots at loony pilot, hitting the cockpit window behind him. Window blows out, aircraft depressurizes, cabin air moisture condenses, etc, etc.
I don't think they shatter into tiny pieces like a car window does.