Personally I prefer
Nathaniel to
Linus, but I don't think
Linus Edmund John sounds bad at all. Remember that middle names are not usually said, they are rarely even read so I don't think it's an issue at all.
If you're not currently planning, I might drop the conversation right now and bring it back up later with an emphasis on
Nathaniel. If he's not changed his mind, then he's not changed his mind