How nice to name the baby after your brother! In my faith, we only name after deceased relatives (no one living), and it's a great honor. I might talk to your parents, but I would bet they would be flattered that you would use the name to honor him. Regardless of situations in which a person passes, they were someone loved and cared for.
My mother named me after her grandfathers and uncle (and yet my name is completely female!). She used the first initials of the men she wanted to honor. If you were nervous about the specific name, you could always use the name's meaning and find another name with the same meaning.