The whole matter is outrageous. There's some more, though, that details the extent of this damage.
The controversy started with the premiere of Gurren Lagann on April 1. After a few members of the 2channel forums criticized the first episode, a Gainax production staffer identified as Keiko Mimori posted an entry in her journal on mixi, a social networking site. According to her April 4 journal entry under the name Kani@Drill Tamashii ("Crab@Drill Soul"), she wanted to survey the reaction to the series premiere. She found a 2channel thread that said the first episode of Gurren Lagann had "C-level animation" and wrote she could not understand the complaints. She then wrote that she "despises 2channel from the bottom of [her] heart" and these "stupid, stupid, disgusting otaku should die!!" Akai, under the name Magi no Suke, responded that personally reading the comments on 2channel was "like putting [his] face next to an anus and breathing deeply."
On April 22, episode 4 of Gurren Lagann aired with pronounced artistic differences from the previous three episodes. Negative reactions filled 2channel's anime boards, the official Gainax blog, and the BBS of that episode's new animation director and storyboarder, Osamu Kobayashi. This led Mimori to post in the mixi journal under the Kani@Drill Tamashii alias that the animation quality had not dropped and that only the characters' appearances and faces changed. She then said that the staffers shouldn't listen to comments from amateurs who don't know better, but only those from anime industry people.
Members of 2channel discovered this later comment on mixi, but their reaction wouldn't develop into a full uproar until after Mimori and Akai's earlier comments from April 4 were discovered. This and the resulting surge in negative responses led to the removal of comments and eventually even main site content from the sites of Mimori, Akai, and Akai's private company Nine Lives. Finally, on April 27, Gainax posted Akai's open letter announcing his resignation, and Mimori and Akai posted additional statements of regret on mixi.
Takami Akai has been a part of Gainax since before its official founding, when he worked on the animation and character designs for the DAICON III and IV convention's opening videos. He was classmates with future colleagues Hiroyuki Yamaga and Hideaki Anno at the Osaka University of Arts. He has been a frequent guest of overseas anime conventions, particularly in California and Germany.
My take is that the other producers and everyone involved with Gurren were going to bail on Gainax if they didn't apologize for this, and in Japanese culture, apologizing comes with someone taking the blame through a resignation. It turns out one of the brainchilds of Gurren (and trust me, a producer has a lot of control over how a show progresses) took the blame - whether he was guilty or not can't really be determined.
It's outrageous that a ravenous pack of idiot, inane otaku could literally force Gainax's hand, when this is the company that loves to screw with fans through teasing or insulting. They've been doing that since 1996, and though I'm not a Gainax fan exactly, I admire how indepedent-minded and daring they can be with money and with their restrictive culture.
2ch has become too much of a "cultural icon" to piss off, apparently, so political correctness has killed another activists entity struggling against conformity in Japan.
A hearty "fudge you" from Terek to 2ch. We bashed you lot well and thorough.