Apparently Stonecipher was a "forceful" leader who was a big proponent of ethical behavior. Nothing in their ethics code (according to notes here) says anything about company-cest, but the board decided his actions would compromise his integrity.
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However, Platt said, Stonecipher acknowledged the affair and the company concluded that his behavior violated a code which states that Boeing employees will not engage in conduct or activity that might raise questions about its honesty, impartiality or integrity.
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"The board concluded that the facts reflected poorly on Harry's judgment and would impair his ability to lead the company," he said.
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You're a leader of a major corporation (you are a leader of any company, for that matter). Poor judgment will inevitably lead to dissention in the ranks. Not surprised they kicked his ass out. No witch-hunting here: Just protection from liability and an effort to skirt anything that might marr the company's already failing reputation.