Just because someone posts a benchmark that is obviously flawed, doesn't mean that someone else should be obligated to do their own benchmark as a counter.
These guys didn't ask for node.js to be used in any benchmark.
The onus is on the person who chooses to do a benchmark, and publish the results, to get it right. If they don't get it right, then they are in the wrong and deserve the criticism that they get as a result.
For example, if these guys were publishing this benchmark as part of a study or argument in a quarterly magazine -- and this was there only opportunity to publish it for the next year or so -- then they would have been far more critical of their own work prior to publishing it. Instead they've quickly thrown together something and pushed it onto the Internet without too much further thought.
So long as it is civil, criticism is fine.