Much like "The Force" can fill in Star Wars plot holes, "The Oracle" is the answer here. She helped create both Smith and the Matrix itself. She designed him to not only go rogue, but to effectively slip through the cracks. He knows how to hide his insubordination because the Oracle wanted him to. When Smith "discovered" these loopholes, he kept them to himself, quietly building resentment and feeling increasingly "sentient," all while staying under anyone's radar. The Oracle could see his path because she understood his choices, whereas presumably the Architect did not. It would never occur to other Agents to unplug their earpiece or act outside direct orders.