It's not a new problem.
You could argue that the original was worded to be deliberately confusing, perhaps even implying that the claims were proven, but I certainly didn't find it that way when I read it.
The stuxnet thing is trickier. To make use of this remotely you (or a stuxnet style virus) would need access to a JTAG connection. These come in many forms, including USB (needing access to the host computer — like stuxnet) or Ethernet (needing access to the network). It seems a bit unrealistic because JTAG tends to be used for development, but field-reconfiguration is one of the advantages of FPGAs.
Of course, I believe this specific Actel FPGA uses flash for configuration, which makes updating it in the field somewhat inconvenient and therefore less likely to be used in practice. I remember hearing that this is why NASA switched to Xilinx, as they now require field reconfigurability.
Still, the article certainly wasn't 'bogus', and the new article claiming so contained far more errors. Especially when you read the actual paper and not just the linked press release.