i think part of the problem is that same-sex relationships are not that numerous in trek lit (certainly there are no prominent main characters that are gay), so when a writer kills of a gay character it tends to stand out more (at least for us gay guys).
You must not have read the Star Trek Vanguard
series — one of its most important characters is T'Prynn, who is a lesbian. And as another poster just mentioned, there was Bart Faulwell in the Star Trek: Corps of Engineers
series; he was a prominent member of the ensemble cast. Both these characters were depicted as having active same-sex romantic relationships. Neither has been killed in their respective series.