My son has his dad's last name. At the time of his birth I agreed that he should have his dad's last name. However, about a week ago, his father assaulted me and put our son in life-threatening danger. As a result the courts have ordered him to stay away from me and our son or risk being re-arrested and jailed. The child is now in my custody, but not through a court order. Can I apply to have my son's surname changed to mine given the circumstances? Or do I still need the father's consent?

You will still need the father to sign off on it too. Why is your custody of your son not through a court order? If the judge ordered him to stay away from both of you then you should have been awarded full physical custody. You should go to court to petition for full physical custody just so you have it in an order. Did you press charges on him for the assult?

He was arrested and charged with domestic assault by the police after he was treated for his injuries at the hospital. Because of the life-threatening danger he put our son in, the CAS was also called in and is now involved: they have made it clear that if I even allow the father near my child for a visit, they will apprehend my son from me without hesitation. The CAS and the courts don't want the father in his son's life: they have deemed him a threat and I rightly agree. Even though the child has been placed in my custody by the CAS and the courts, I have begun the formal process of suing the father for temporary and permanent custody as well as for child support as a means of throwing my support behind their decision as well as to ensure the long-term protection of my son's well-being going forward into the future.
In the meantime, the court has also ordered the father to stay away from both of us or face immediate re-arrest and stiff jail time.
Given the extreme circumstance I no longer want my son to have the father's last name. I know the father of the child will never agree to let me change his surname to mine, so I wonder if I any other options? The idea that his name will linger with questions like "why is his last name different from yours?" for years to come bothers me. I don't like the idea of having to explain that one. My intent is not to sneak away with the child but to claim him as my own with my surname: I don't believe that his father should have naming rights to our son after he treated us the way he did. The bottom line is: I don't want my son's life to be complicated by this situation as he gets older.

What state are you in? Each state has their own set of laws regarding cases like these and even the ones without actual laws have "historys" or "case-law" based on how the court has ruled on similar cases before yours. That will make the most difference right now. I could go on about many different possibilities but it would save a lot of time if we could address just your state.