As he said, that omission was "not a forward thinking decision" (gee . . . you think?). He said it came about largely because The Next Generation "was a syndicated family show" with affiliates to please, but I'm not sure how much weight that carries, especially when applied to the likes of Voyager, Enterprise, or DS9 (which was especially edgy, compared to the rest of the Star Trek universe). Regardless, you can read the entire interview over at After Elton, although there's really not much more to it than that.
Sadly, for all the efforts he's put into "watching" Star Trek, it seems he has never taken the time to "read" it. If he had, he'd know that writers of the novels have been taking significant steps towards promoting equality within their visions of the future, including some very positive representations of LGBT characters and issues. In many cases, it's just a one or two page background reference to a character, with their gender/sexuality of no more significance than the colour of their eyes, but there are some more prominent relationships.
While the below is by no means a complete listing, it's a good place to start for anybody desiring an 'alternative' read of Star Trek:
- A Stitch In Time by Andrew J. Robinson: Written by the actor who played Garak on DS9 (and who has admitted he always played the role as if Garak were bisexual), refers to a past attraction to a handsome Cardassian male.
- The Best and the Brightest by Susan Wright: Written by an openly bisexual author, it features a lesbian relationship between Moll Enor (an unjoined Trill) and Jayme Miranda (a human).
- Blackout by Phaedra M. Weldon: Dr. Bart Faulwell flirts with an Asarion, an alien race that can switch sexes.
- The Buried Age by Christopher L. Bennett: References a lesbian couple who are married, share a last name, and are raising 2-year-old son. In addition, the story features an alien race called the Manraloth who can transform their bodies (including altering their gender).
- Dark Passions 1 & Dark Passions 2 by Susan Wright: Written by an openly bisexual author (see above) and set in the Mirror Universe, the first features Kira as a bisexual villainess and Seven of Nine as a lesbian agent who seduces her. The second features an equally bisexual Deanna Troi who romances Kira.
- Deny Thy Father by Jeff Mariotte: During his Academy days, Will Riker and a female classmate named Estresor Fil competed for the romantic attentions of another female classmate named Felicia Mendoza.
- Destiny 1 (Gods of Night), 2 (Mere Mortals), and 3 (Lost Souls) by David Mack: Ranul Keru (see Section 31 below) features prominently in all 3 books. In addition, book 1 references his boyfriend Sean Hawke, while book 2 has an interesting dialogue about lesbianism)
- Forged in Fire by Michael A. Martin & Andy Mangels: Reveals that gay marriage is commonly accepted among Klingons.
- The Good That Men Do by Michael A. Martin & Andy Mangels: During a discussion, it's revealed that Trip's brother, back on Earth, has a husband.
- Harbinger by David Mack: The Vanguard series, which begins here, features a female Vulcan officer who is engaged in a lesbian relationship with a female Klingon spy, who is disguised as a human. T'Pryn goes on to appear in Summon the Thunder, Reap the Whirlwind, Open Secrets, Precipice, and the Sorrow of Empire Mirror Universe novel.
- House of Cards by Peter David: Burgoyne 172, a recurring bisexual character in the New Frontier series, is established here as a Hermat (a race of hermaphroditic aliens).
- Kobayashi Maru by Michael A. Martin & Andy Mangels: Makes reference to a married gay couple.
- Mission Gamma: Twilight by David R. George III: Etana Kol and Kristen Richter are established as a lesbian couple and appear in several of the DS9 relaunch novels that follow.
- Obsidian Alliances by Peter David, Keith R. A. DeCandido, and Sarah Shaw: Sarah's contribution to this Mirror Universe collection, Saturn's Children, reveals that the alternate-universe Leeta and Ezri are married.
- Over a Torrent Sea by Christopher L. Bennett: Features an alien race with four sexes, two of which are male, and two of which are hermaphroditic.
- Pathways by Jeri Taylor: Reveals that Harry Kim's Starfleet Academy roommate was not only a gay man, but one who was in love with Harry (although Harry isn't gay, they remained friends). In addition, Brad Harrison and Noah Mannick are established as a gay couple aboard Voyager.
- Renaissance by Peter David: Part of the New Frontier series (which also features Burgoyne 172), the novel introduces the gay Vulcan brother of one of the lead characters, who is unique as much for his sexuality as for the fact that he's immune to the Pon Farr mating ritual.
- Section 31: Rogue by Michael A. Martin: Lieutenant Sean Liam Hawk and Ranul Keru are introduced as a gay couple (although Hawk was killed off in Star Trek: First Contact, Ranul has reappeared in several DS9 and Titan novels).
- Serpents Among the Ruinsby David R. George III: Gell Kamemor, the female Romulan ambassador, is revealed to have a female partner named Ravent, with whom she raises their son.
- Shards and Shadows edited by Margaret Clarke and Marco Palmieri: Rudy Joseph's contribution to this Mirror Universe anthology, The Sacred Chalice, features a closeted gay male Cardassian politician.
- The Star to Every Wandering by David R. George III: References a female starship captain by the name of Margaret Sinclair-Alexander, who is involved in a lesbian marriage (leading to the hyphenated last name).
- The Sundered by Michael A. Martin: Ensign Pamela Hopman is established as female-identifying member of an androgynous species that changes genders regularly.
- To Reign in Hell by Greg Cox: It's revealed that two of Khan's male followers are married, and that the camp's primary physician is gay.
- War Stories Book 2 by Keith R.A. DeCandido: Relates the first meeting of Dr. Bart Faulwell and his boyfriend, Lt. Commander Anthony Mark. Bart is a regular character in the Starfleet Corps of Engineers series, and their relationship is mentioned regularly).
I'm sure there are even more instances, particularly in the off-shoot sagas (New Frontier, Vanguard, Titan, etc.), but the books are ones that I've been keeping track of for myself. There's still never been a mainstream Star Trek novel with a LGBT main character on the bridge, but the groundwork has been set.
Keep an eye on the likes of Susan Wright, David R. George III, Michael A. Martin, David Mack, and Keith R.A. DeCandido especially, and I daresay the day will come . . . hopefully sooner, rather than later.