Is it permissible for us to stop our stepmother at her limits, knowing that she controls our father and instigates problems between us and him, and that our father might react with anger?

You must be dutiful to your father and avoid harming him, especially in his old age, in accordance with the Almighty's saying: "And your Lord has decreed that you shall not worship except Him, and to parents, good treatment." Patience and forgiveness are due to the father's wife, while retaining the right to self-defense and to present your argument to your father. Furthermore, one must beware of harboring ill suspicions about Muslims without justification, as the Almighty says: "O you who have believed, avoid much [negative] assumption. Indeed, some assumption is sin."