Though this might be true about the article itself as posted, this is not a bit of bad journalism. The author Sydney Finkelstein, is a Professor of Management and spent 6 years studying 50 companies and conducting some 200 interviews, here's a link to the journal article : http://www.jacksonleadership.com/pdfs/7Habits_IveyBusinessJo...
So to answer your "If you really wanted to check the effect of a certain character trait, you'd need to try to (carefully) compare how CEOs with the trait performed compared to CEOs without the trait, and make damn sure your sample sizes and methods are sound before making any confident assertions." It seams like 6 years, 200 interviews, and research in 50 companies would seem to be a fairely extensive study IMHO.