Seems awful trivial five years later. Givewell does excellent nonprofit analysis, and they don't seem malicious or unethical in any way that I've seen.
Yup. It's unfortunate that this still dogs them in internet forums, but it's really only on internet forums where someone always insists on bringing it up.
One thing I love about GiveWell is that they publicize and learn from their mistakes, this one included. http://www.givewell.org/about/shortcomings They're really, really good people. Like everyone, they did something dumb. Unlike most, they learned from it and spend their lives trying to improve the world.