Complicated family stuff: my brother is an athiest

Well, here I sit, waiting to become an Aunt (my sister in law is in labor right now!) thinking about how having kids is such a big deal and huge responsibility. Parents have to care for this little baby and feed it and tell it bedtime stories and instill manners and give it toys that aren't made in China ... and even if you do all that the right way they might grow up to be an axe murderer or a Scientologist and then everyone blames the parents. And it's more than just blame. I imagine the parents feel a certain amount of guilt themselves, even if their child's foibles are no fault of mom and dad, and certainly parents still worry. I only know one set of parents (mine!) who stop worrying about their kids once they turn 21, but my parents have an excuse because they have so many little kid at home to worry about. That does leave me to do a lot of the worrying, though.
My big worry right now is my little brother Joey. That's his real name, sorry Joey, I'll protect random strangers on this blog but not you kiddo! It's the price of being in the fam, tough luck.
Anyway, Joey was always a pretty good kid after he emerged, butterfly-like, from an extended "terrible twos" phase that lasted until he was 9 or 10. He did his homework, won local races, volunteered at his local church, learned to garden, had a steady job with a landscaping business where he was rapidly promoted and well-liked. He saved up cash for college, left the cramped and oppressive nest I call "The Compound", and went to school to major in botany, since he had quite a green thumb. Along the way, he took a biology class, fell in love with Darwin, and - quite suddenly - became an atheist and stopped speaking to the rest of the family.
How to respond? This is creating big waves in the family. We're pretty conservative: one brother's major is theology; we all fall into one or another Christian denomination; for a while my parents didn't even have a TV (aka Satan Box). Joey bid us goodbye with a quick "I don't have time for ignorant people" kind of email, but I think the best response would be an email or call to say "I still love you, call me sometime" and avoid the entire topic for now. After all, he's a college freshman. Chances are excellent that he'll grow out of this. I feel like letting it lie. But the problem is not all family members think this way. My brother in law, who frankly irritates the crap out of me, sent Joey a long and irate email that completely sidestepped the issue and focused instead on the "ignorant" slur. PUH-lease. Some college kid called you ignorant, so what, get over it. Most college kids think everyone else is ignorant. And thanks for alienating my brother, bright stuff.
So things to ponder as I formulate my response to Joey:
1. This change is not unexpected. My parents have fallen into religious extremism at times, so this is a typical rebellion.
2. I may need to undo harm done by bro-in-law
3. Establishing contact is the first step
4. I just want to be talking to him again and help him understand his decision doesn't make him the enemy. We can disagree for now and get to the bottom of this later (yeah he's entitled to his opinion but I am a Christian and do want to have my say eventually! Just not right away!)

Ok, advice welcome! Help me handle this one!