Misinformation is the cancer killing /a/.
a) The problem wasn't 2ch "trolling" GL, the problem was Takami Akai, a producer NOT THE DIRECTOR, defending the criticisms of a girl animator saying how "people don't understood episode 4". He said those that complained are idiots and reading the comments was like "putting [his] face next to an anus and breathing deeply." After people became aware of his comments, he "resigned" from Gainax.
b) Imaishi was always director of the show. Hell, he even directed the pilot on Abenobashi episode 3 and has hands-on for Gurren-Lagann 27.
c) Takami Akai himself was still working in the show and he was still a part of Gainax. He was just not credited.