I'm fine with it, as Kirk obviously became even closer to Spock than he was with Gary Mitchell.
And really, referencing Gary Mitchell or Edith Keeler during that moment in TWOK adds absolutely nothing. The movie needs Kirk to be utterly shattered by Spock's death at that point in the story. If Kirk mentions Gary, or Edith, or even his brother Sam for no other reason than to tick off some boxes for the hardcore fans, it distracts you from Kirk mourning Spock's death and makes the more casual viewers go, "...Huh? Who are Gary and Edith? When did they die? Did I miss something?"
Because honestly, as awful as their deaths may have been for Kirk personally, for viewers, Gary Mitchell, Edith Keeler, and Sam Kirk were all just one-episode tragedies that were never referred to again onscreen. Spock was Spock. We'd been with Spock for 16 years by that point, the same as Jim Kirk. We knew and loved him just as much as Kirk did. Spock's death, and Kirk's reaction to it, was what was important.