"I think that those critics make two mistakes. First, they implicitly presume that there is an unchanging conception of theory confirmation that can serve as an eternal criterion for sound scientific reasoning. If this were the case, showing that a certain group violates that criterion would per se refute that groups line of reasoning."
Showing a line of reasoning doesn't conform to current requirements of scientific reasoning does not refute that line of reasoning at all. It simply indicates the line of reasoning has an extremely heavy burden to convince other scientists of its truth. In other words it states the line of reasoning is incomplete, not necessarily wrong.
I do think it is a hard sell to proclaim a theory the true picture of nature when you can produce no empirical evidence beyond the fact that the equations match the data.
String theory, for example, requires several extra dimensions to provide accurate results. If strings are real, the dimensions must be there. If not, the extra dimension are just "fudge factors" used to create a way to calculate the correct results but with no basis in nature. We won't know if String Theory is true or not until someone can crack the extra dimension puzzle.