A lot of the strong feedback appeared to be a backlash to the perception that this was a marketing scheme dressed up as a public service suggestion. Offering an open letter of advice coupled with biting critique, rather than making a private offer, does strike a certain self-serving tone. While I generally love seeing how designers would, free of real-world constraints, re-imagine popular sites, maybe the authors didn't choose the best tone or format for their submission.
Yes, there's been a trend recently of "I'm redesigning X, completely from scratch, because it needs it" with the implication that X's current design is badly in need of improvement. This is going to bring the designer both positive and negative attention, and deservedly so. Typically the redesign is radical and makes bold, often false assumptions about the product, which makes these posts seem particularly self-serving.
I think that these designers could do just as good a job of demonstrating their creativity by using a fictitious brand (and possibly even drawing comparisons to known brands in the article). It is not classy to drag someone else's brand through the dirt.
I think the response would have been different if the design firm had openly approached the Wikipedia community at the beginning of their project to offer their pro bono services. Instead it seems like the designers did the work in isolation for 2 months and then sprung it on the world--not a very collaborative working style.
I believe most design firms offer some kind of prototype as a first step, which is what they did. They weren't commissioned to do anything, and there is no go-to person at Wikipedia for them to work with; an iterative process would have required working with a democratic committee of volunteers who individually don't have the authority to make any kind of decision.
I've hired a lot of web design firms over the past decade and I've never seen or requested a 2-month-long prototype phase as the first step.
The first step in a web design project is always discovery, so that the design firm does not waste their time (and my employer's money) on work that does not solve the right problems, or cannot be implemented.
Ad agencies, in contrast, will typically come to a pitch meeting with some concepts or prototypes. But that is ok because ads are self-contained products that are largely free from legacy systems.
I do really enjoy seeing creative individuals do unrequested design comps, but I think you hit the nail on the head: Don't drag someone else down to do it.
That said, when I find myself typing something venomous (more often than warranted), I try to take a breath and delete. Worked for Lincoln: http://www.examiner.com/article/an-unsent-letter