Would it be considered an act of disobedience if I were to tell my parents that they are mistaken in their treatment of my wife, knowing that I always take their side over hers?

Supporting both the oppressor and the oppressed is a religious requirement. Supporting the oppressed means removing the injustice from them, while supporting the oppressor means preventing them from committing injustice. This is based on the Prophet Muhammad's (peace be upon him) saying: "Support your brother, whether he is an oppressor or oppressed." The support for the oppressor was interpreted as restraining him, meaning preventing him from committing injustice. Disagreeing with parents and clarifying the truth to them with politeness and gentleness is not disobedience; rather, it is a form of showing kindness to them, as Allah Almighty says: "And your Lord has decreed that you worship none but Him, and to parents, due kindness."