A committee requires two witnesses or a confession in the presence of the committee. Your uncle only counts for one, but if you tell him you don't believe in god, and you tell another family member later, even though you told both individually that counts together as two witnesses if they both run to the Elders. Keep that in mind. Your uncle doesn't need to run to the Elders. He is one.
Look, you're getting a lot of advice and I'm giving you advice too but here's what it comes down to, you need to trust your gut because you actually know the guy but also think ahead about what you want to come out of this. Are you looking to feel better? Most likely if you're honest with the guy he's gonna make you feel worse. Are you looking for affirmation? He's not going to give it to you. What do you hope to come out of the conversation with him?