Just be sure that you're really going the atheist route before you say anything. I told my mom that I was an atheist in college, and she took it pretty well, but I'm finding myself drifting back towards Christianity, and she doesn't seem to understand. She'll still make cracks about her "Godless heathen son", all good natured, nothing nasty, but it's really hard to take the atheist card off the table once it's out there.
You may want to approach it less directly than blurting out "I'm an atheist!" Maybe try explaining to him that you feel religion is too important to blindly follow what someone else believes, that you're working on making your faith even stronger by really re-evaluating what you believe, and that, while you appreciate what he believes, that this is really something you need to work through on your own. This will either get him off your back about the whole topic, or at the very least, allow you to ease him into the topic at your own pace.