I actually have a guy FBF in Chicago (he's a COGIC elder, brother of a friend of mine here in Atl) who has a ministry page designed to interact with/debate with/answer questions from atheists. I tried to help him out a few times, but I was in way over my head because he has a lot more patience than I do. Those people can be brutal.
I would say it's a good idea to unfriend if that's not your thing, but I wouldn't want to give the impression that we should automatically unfriend anyone who doesn't believe in God. You never know how He might use you.
Personally, I'd just hide him from my news feed so that he can see every time I glorify God, but I can't see any of his folly. 
He's more patient than I am.
My general grievance with atheists is that they are some of the most condescending people I've ever spoken to. Those are people I pray for that the Lord would reveal himself to them because speaking to them is generally a waste of time.
Catholics have beliefs. Jehovah's Witnesses have beliefs. Pentecostals (which I am) have beliefs. Baptists have beliefs.
Atheists? Their 'beliefs' are founded on everyone else's beliefs being false. As such they study and learn to debate and debunk everything we believe, so they revel in an opportunity to tell us how illogical we are. They glory in their 'logic' and their superior 'intellect'. They read the bible to debate. They look for historical inconsistancies. They are the must frustrating people to talk to because you get the sense that they're trying to look down on you. As if you're speaking of make-believe and fairy tales and they're trying to 'enlighten' you.
A fool hath said in his heart...
