Speaking purely for myself as an OTW staffer (do not speak for the org here), we really do want to know what we're doing wrong if anyone's willing to tell us. We can't promise to fix it — some of what people get offended by in our work is a deliberate choice, for example, our refusal to link explicitly and publicly the Board members' legal names and fannish pseudonyms — but we do want to know about it. And OTW staff, volunteers, et al., are not a monolithic block; you know that old line about "two Jews, three opinions"? Well, I have come to believe in "two fans, seven opinions." There are parts of the mission statement that I, and I believe some other staffers, are not thrilled with, and while I doubt that will change anytime soon, I don't think much about the org is set in stone.
More to the point, and less repetitiously, I can promise you that if you want to ignore OTW, we are not going to come to your journal/website/whatever, and force you to upload stories to the Archive of Our Own at gunpoint, contribute to Fanlore, anything like that. If you want to use the website, participate in any of the activities we host, check out the Fanlore wiki, read Transformative Works and Cultures, get support if you get hit with a C&D, we're there. You don't need us? Have a great time in fandom, Stargate: Atlantis spoilers are thataway, and fandom_wank has some mind-boggling Jensen Ackles stuff going down today. We can't do anything about our supporters talking about us (although dear god I would love to stop people from spreading misinformation in their enthusiasm), and we're honestly pretty thrilled that people are interested in what we're doing. So, you know — I can't in all honesty apologize for the fact that you've encountered evidence of OTW's existence, but feel free to ignore everything you see on the topic, and also please feel free to drop me a line on any of my public posts or email me if you want to talk about the topic (or tell me to fuck off, that's also totally an option).