There's a tendency of people with an association with the Wikimedia movement to see it as a hammer that can be swung at every nail. This is embodied most perfectly in the e-mail by Rebecca O'Neil, who claims that if WMF doesn't take a position on any issue (or every issue?), it is taking a position in support of the status quo.
That is absurd. The movement and the WMF have a purpose. That purpose is not koala habitats, nor Superfund sites, nor opioid addiction nor LGTB rights in Uganda. All those issues are valuable purposes for an organization to have, but the WMF has a different purpose. Its activities should be in pursuit of its mission. Not any and every mission that at least some Wikimedians think is valuable.
All that said, how many views did the wikimediafoundation.org site get during the time the banner was up? A few hundred? A few thousand? Varnum apologized, the banner was a bit of a rush job. Rather than arguing why WMF should support all your pet causes or, alternatively, hand over the keys to "the community" - maybe just move on.