It's not about calling the entire peer review system into question - it's about being skeptical about whether or not results can be trusted on the sole basis they've been peer reviewed - particularly in areas of scientific controversy.

From the linked article: "As Climategate has shown, [the process of peer review] became compromised – causing an instability. As seen in the leaked emails, many within the climate establishment were interrelated and working together to ensure their message of global warming wasn’t diluted. There were even desires to redefine the peer review literature to punish journals that published skeptic’s papers."

It's not just climate science (as I've been reading on nutritional science with Gary Taubes and Robert Lustig).

Definitely not - you misunderstood. The leaked emails and this story are just the beginning of the process of uncovering the greatest scam/racket in recent history. And I assure you Sir, that these Indian dudes are not the last to have their names dragged through the mud (and more, I expect). Too much public money and trust has been wasted by these shameless scoundrels.