Was Kirk's retirement from the Star Trek franchise already decided in The Undiscovered Country?

According to the Development section of the Wikipedia article for The Undiscovered Country:

With the looming 25th anniversary of the original series in 1991, producer Harve Bennett revisited an idea Ralph Winter had for the fourth film: a prequel featuring young versions of Kirk and Spock at Starfleet Academy. The prequel was designed to be a way of keeping the characters, if not the actors, in what was called "Top Gun in outer space".Bennett and The Final Frontier writer David Loughery wrote a script entitled The Academy Years, where Dr. Leonard McCoy talks about how he met Kirk and Spock while addressing a group of Academy graduates.

So the first idea was to keep the TOS characters, but not the crew. This was rejected:

Actor James Doohan claimed that Paramount chief Frank Mancuso had fired Bennett following negative reaction from the core cast, Roddenberry, and fans. Bennett claimed that after he rewrote the script to include Shatner and Nimoy, Paramount had still rejected it and that he decided it was time he left the franchise.

A second idea of a (almost) total party kill was presented by Chekov, also not used:

Actor Walter Koenig approached Mancuso with a new script outline codenamed "In Flanders Fields"; in it, the Romulans join the Federation and go to war with the Klingons. The Enterprise crew, except Spock, are forced to retire for not meeting fitness tests. When Spock and his new crew are captured by a monstrous worm-like race of aliens (which Koenig described as "things that the monsters in Aliens evolved from"), the old crew must rescue them. In the end, all of the characters except McCoy and Spock die.

In the end, Nimoy was asked to write.

Mancuso asked Leonard Nimoy to conceive the new film to serve as a swan song for the original cast. Nimoy, Mark Rosenthal and Lawrence Konner suggested Kirk meeting Jean-Luc Picard, but Star Trek: The Next Generation??'?s producers refused to end their show. ... Ralph Winter was brought on to the project as producer shortly after Bennett's departure, and said Paramount's mandate was to produce a 25th anniversary film that would not cost a lot of money.

Mancuso being the Chief of Paramount at the time. A swan song being the final movement made before death/retirement. So the answer was yes. This is backed by the DVD extras and Shatner's mémoire (From Memory-Alpha):

The Undiscovered Country was almost never made as a Star Trek film, not only due to the dismal box office receipts of Star Trek V: The Final Frontier, but also for an unbroken string of, for Paramount Pictures, disappointing yet very expensive movie releases as well, leaving the studio deeply in the red, only aggravated by a worldwide recession. However as seen on the Star Trek VI DVD set and also according to William Shatner's Star Trek Movie Memories, Paramount, specifically its president Frank Mancuso, Sr. – who had been intimately involved with Star Trek ever since Star Trek II: The Wrath of Khan – , did not really want to end the Original Crew run on The Final Frontier low note, especially with the 25th Anniversary coming up, and wanted one more film.

So already knowing that this should be the last TOS movie, Nimoy, along with Nicholas Meyer, who directed The Wrath of Khan and co-wrote The Voyage Home ended up spitballing until they got the final idea of not so Cold anymore War in Space..

Remember, the movie before, Star Trek V: The Final Frontier, was a failure, and the success of TNG was already calling for an end to the TOS series, so Undiscovered Country was more like a retirement gift to the series than anything else.

That said, Generations turned into an epilogue for Kirk, when production of Generations was denied the killing of a TNG character. Initially, the plan was a prologue cameo instead of a main role. From the Generations Wiki article:

[TNG director] Berman felt that including the original cast of the previous Star Trek films felt like a "good way to pass the baton" to the next series. In the initial draft of the screenplay, the original series cast appeared in a prologue, and Guinan served as the bridge between the two generations. [...] Moore recalled that "we wanted to aim high, do something different and big... We knew we had to have a strong Picard story arc, so what are the profound things in a man's life he has to face? Mortality tops the list." After the idea of killing off a Next Generation cast member was vetoed, someone suggested that Kirk die instead. Moore recalled that "we all sorta looked around and said, 'That might be it.' " The studio and Shatner himself had few concerns about the plot point.