I am very sorry for your mum, you and your whole family. I wish you all the strenght you need.
But why not Nathaniel? It sounds a bit differnt than Nathan, so hopefully you won't associate it with your ex-boyfriend too much, but I'm pretty sure it means the same. You could always looks for differnt names with the same meaning (like Jonathan or maybe Isidore is nice. It means gift from Isis, the egyptian godess).