I agree about the emphasis point. That's why we almost always hear people talking about man being descendant from apes, while we almost never hear about man being descendant from bacteria.
Although I don't think it's so much worry about turning atheists away from evolution (although that could happen with some), but I think its more about the worry of turning the general public away from evolution. And if that happened it would give more strength to religion in society, which many secular forces simply don't want to happen.