What are you talking about "persecuting because of another's non-belief"? Non-belief is simply the result of critical observation and logic. There is no evidence for any of the superstitious claims, and those claims are hinderances to morality. Wnen people actually let go of their superstions they're left only with what really is, and that's what we need in order to make rational decisions - a superstition free world view. It doesn't mean that being an atheist makes you good by default, it just means belief is not rational, and can only at best clould one's ability to make moral judgements.
When you get down to the nitty-gritty of it, you're basically saying:
Belief = Immorality
Non-Belief = Morality
And I heavily disagree with that. I agree that religions can be used to justify immoral actions. And I agree that non-belief (statistically, at least) does probably encourage morality (US Prison stats for example).
But I don't agree that there is a direct correlation. If a religion can justify immorality to a gullible theist, you need to ask questions like "Is it because the theist intentionally wishes to hurt and destroy, or because they have been duped?". The former is immoral, the latter is not necessarily immoral.
I think there is a strong correlation, but not a direct correlation.