I believe there was a GAF thread when the study came out.
Searched for 'e-ink', 'e-reader', 'strain'; no dice.
So I decided to do my own (secondary) research:
In 2000, a study in Industrial Ergonomics showed that light reflection and polarization played a large role in eye fatigue. Their results show that glossy screens are more likely to cause fatigue than matte screens.
In 2004, a study published at International Display Workshops found no difference in eye fatigue between e-ink and printed paper.
In 2006, a study from Duke University published in Radiation Imaging Physics argued that one cause of eye strain is from a process called luminance adaptation (this may not be the primary source for this theory). In a nutshell, it suggests that using an LCD in a dimly lit room causes eye strain by this mechanism. LCD's in brightly lit rooms (or ambiently lit screens like e-ink) would not cause strain by this mechanism.
A 2009 study published in Displays showed no statistically significant difference in subjective reports of eye fatigue among 48 participants when comparing two different e-ink displays to paper; this study also compared resolutions of 800x600 and 640x480 and showed that although visual performance increased (finding a specific symbol in a string of letters), there was no effect on eye fatigue. This suggest that "Retina" displays probably won't make much difference in terms of fatigue.
I did not find any studies that compared e-ink to LCD for eye fatigue.
Based on what I did find, I would tend to believe that e-ink devices would cause less eye fatigue than the iPad for the following reasons:
1. e-ink devices always use ambient lighting, so there is no luminous adaptation required.
2. e-ink devices use matte screens, whereas the iPad uses a glossy screen.
It does seem that you can accommodate your iPad use to mitigate these effects if you only read in brightly lit rooms and position yourself to minimize screen reflections.
Still, I would be interested to see an actual study comparing the two technologies head-to-lead using identical lighting conditions and tests that were more akin to the practical application (i.e. reading a chapter of a novel).