According to the report on the CBC about this:

"Hamlin said she told the woman she had nipple piercings and offered to show them to the female agent in private. But male TSA officers insisted she remove the jewelry before boarding her flight" (emphasis mine)

and as it's pretty clear in both HN and the cbc coverage, Hamlin offered to have a visual inspection, even though she wasn't offered one, and was denied.

Furthermore, a friend of mine who's been following the case says that they only asked her to remove her nipple rings and not the belly button piercing or any other piercings, which seems awfully strange if it's for security reasons.

And the TSA have the gall to insist their "security officers are well trained to screen individuals with body piercings in sensitive areas" (TSA statement)?! This is awful.

The argument that it's not natural, so such invasions of privacy, deprivations of dignity and pain - NIPPLES, people! - are justified is not a good one; we do all sorts of unnatural things to our bodies, for aesthetic and practical reasons. I don't think you could engage in any body modification that would call for the behaviour reported here.