Perhaps his deceitful ways are what enable him to be the great GM that he is. Even in the human body, the sphincter has its purpose.
Even when he makes mistakes (Bichette) he somehow turns them into gold. (Reitsma) If we replace him with a lesser GM, will the extra money be wasted? How much of Bowden's success can be attributed to his talent scouts, coaches, and other parts of the organization? I don't know, but I certainly hope we don't find out the answers AFTER the fact.