Do you think it's wrong of me to unfriend my long known friend?
Why do you want to unfriend someone youve been friends with for so long?
I don't know how he got on my facebook timeline
You have full autonomy over your facebook timeline. If you have friends on there that you dont want on there then you are completely free to make the change.
Ok I'm going to unfriend my best friend.
Do you have a specific reason why you are removing someone that you're now referring to as a best friend? While you have full control over who you add or remove from Facebook, you could be hurting his feelings by removing him without letting him know why.