Some thoughts.
I don't see the problem, myself. There's no product, service or
commercial interest being advertised. It's for users who are logged in, not all readers. People who choose to participate actually receive money, which can then be donated to the IRC or Wikimedia.
Advertisement doesn't need to be commercial. In fact the idea of advertisement is as much about raising profile as it is about selling a specific product.
Harvard (for example) is essentially a commercial entity, and having their logo at the top of Wikipedia pages (even if it is just for logged in users) is good advertising. As is the potential of being seen linked to Wikipedia.
There has also been suggestions that the Berkman Center has existing links to the foundation - I've not picked up what those are but if it involved funding that adds even more of a twist. (some hints on what connection exists would be useful :)).
I think another concern is; why is this something WP wants to support? does it help our goals? Does it advance anything?
Yet other objections are based on privacy concerns (over being redirected to a third party website)... Such concerns are so overblown, I'm tempted to advise those who raise them to switch off their cellphones and disconnect their modems lest the Illuminati (or Fox News) use these signals to remote into their brains.
I do not think these concerns are initially unreasonable. Within the community exposing someones identity, details or IP without consent is strongly frowned upon. I don't think it is problematic to object to any sort of link being made.
Obviously that issue has been assuaged, and it appears the researchers took major steps to remove the IP link concern (praise to them for that).
The extension to this objection is that none of this is detailed *before* clicking the link (or after it, really). So the access path could be improved dramatically.
If I'm honest, I think most people are just upset that someone didn't personally ask them first.
I'm not sure why you pitch this as an invalid problem :) It's certainly my only concern, especially as the community objected in the first place with advice to seek support from RCOM and the Foundation.
I realise in doing so we may have made our own bed to lie in... but I also do not think it unreasonable to expect RCOM to come back and *inform* the community of what is about to happen.
This is once again and example of the meta level organisation making community level decisions without any input. Not a good collaborative situation!
Tom