Get in an aircraft with flare launching capibility.
hint format ["%1", (vehicle player) weaponsTurret [-1] ];//gets the weapons for the pilot, check to make sure "CMFlareLauncher" is in this list.
(vehicle player) removeWeapon "CMFlareLauncher";//This command should theoretically remove the flare launcher, as you can remove any weapon found in "(vehicle player) weaponsTurret [0]"