Does not naming a newborn "Yusuf" – in accordance with the mother's wish – constitute disobedience, given that there is a vow to name him "Muhammad"?

You must fulfill your vow to name your newborn Muhammad, because fulfilling a vow is obligatory, and naming a child Muhammad is recommended. Your disagreement with your mother in this case is not an act of disobedience; for obedience to parents is in what is good, not in abandoning an obligation. You should be gentle with her and explain the reason for your action, while continuing to treat her with kindness and beneficence.