First, the paper appeared in a journal called Footwear Science. This is the belly of the beast, as it were, a journal from the footwear industry, not some hippy-dippy barefooter.
Second, the paper was given the Nike Award for Athletic Footwear Research for 2009:
"The winning study addressed barefoot walking in a habitual barefoot population from South India. Results showed that habitual barefoot walkers had subtle (but probably desirable) differences in foot form (i.e. a wider forefoot) and plantar pressure (i.e. better distribution) when compared to habitually shod peers. These results strongly suggest that everyday footwear should respect the foot's natural form and function."
Yes, that award is from Nike, the sneaker company.
Third, the key paragraph from the study ends with the killer observation (emphasis mine):
"While such populations are relevant in a clinical and applied context, one aspect should be borne in mind: the habitual use of footwear from early childhood may influence the shape, and probably the function of the foot. Traditional Chinese foot binding (Jackson 1990) is an extreme example showing that the human foot is a highly plastic structure, but even everyday footwear influences the foot. Studies on Chinese (Sim-Fook and Hodgson 1958) and medieval British populations (Mays 2005) found foot deformities resulting from restrictive footwear, but even recently in the USA, Frey et al. (1993) reported that 88% of the healthy women surveyed were wearing shoes smaller than their feet, and that 80% of them had some sort of foot deformity. A relevant question therefore is: is the Western foot, used in most studies, not ‘natural’ any more, and is our current knowledge of foot biomechanics clouded by the effects of footwear – in other words, are we studying ‘deformed’, but not biologically ‘normal’ feet?
"This may be considered likely, when confronting two palaeoanthropological findings...."
Nike gave this paper an award, remember.
It's here, in PDF. Read the whole thing.