Dan (aka:vilesilencer on most forums) made a similar point. His own sampling was a hand-picked list of directories he feels make the cut for quality... and you can find that list on his forum: Free Directory List - Top 100 Free Web Directories .
His point was the Schwartz post was apparently based on a WMW thread where a guy announced the ones he'd tested had a large percentage of de-indexed sites. Who knows what list the guy was working from. Dan's handpicked list had a zero percent fatality ratio, and that speaks to the idea that quality directories DO see a different treatment than others.
Not suggesting the current algorithm is perfect by any means, just saying the idea that free directories are all toast is just hype. It might make good linkbait to announce things like that, but so far it appears to be statistically flawed.