Hi etcnepal,
Thanks for posting this. Is the blog post yours?
The issue of Flickr suspending the account because of suspected activity is unfortunate. Without having any more information than is provided in the blog post, it sounds like Flickr made a mistake.
The issue of organizational accounts is a little more nuanced. It is true that Flickr accounts are intended for individual users, not organizations. This is explained in the product description for Flickr's donation at TechSoup, and it's also the reason why the donated accounts come in bundles of two and five.
More importantly, using one account for an organization really isn't the best use of Flickr. A group page is a much more elegant use of the technology. The group page allows volunteers and other friends of your nonprofit to add their own photos of the work you're doing. The group also includes a discussion board and other social networking features. You can moderate groups too.
The blog post says, "I could not find anything to show they have done this to a large or well known organization such as several of the Children’s Hospitals, and large congregation churches however when it comes to small groups with little to no national recognition they seem to not care." I certainly hope that this is not true. I suspect that many of the larger organizations the person was referring to were using organizational groups rather than organizational accounts.
Hope this helps,
Elliot