Yes, Logan was respecting Scott and Jean's marriage as far back as the 90s. I referenced Morrison's run as the last time that happened but it was just once in many instances when Logan had already done that. A lot of people see Logan not attending Scott and Jean's wedding, and not knowing the context, they assume it's because he couldn't bear to see them married when it was really just because of Fatal Attraction. And even in Claremont's original run, after Logan meets Mariko and thinks Jean is dead from the volcano attack against Magneto, Logan even reflects on how he doesn't love Jean anymore. Mariko is the woman for him. Even in TDPS, Logan reflects on how he loved this woman with the emphasis being on past tense.
The love triangle was somewhat revived by Claremont from the Classic X-Men backstories but even then, those stories were set in the past and didn't really affect the present (even if Claremont would have broken up Scott and Jean and paired her with Logan like he did in X-Men Forever had he stayed on through the 90s and gone ahead with his Dark Wolverine Saga). The love triangle ceased to exist until TAS which was a new continuity and then the movies. UXM 394, which featured the Logan/Jean kiss on the cover and in the interior, was published directly after the success of the first movie. The comics definitely took a lot of direction from the movies so you can see that the movies are what really inspired the return of the love triangle and trickled down to the comics and shows like WATXM. And that's why for the general public, Wolverine and Jean have become the main couple (which seems to be carried on over to the upcoming Wolverine video game). In the Hulu show, The Act, the main character is wearing a red wig when she attends a comic-con. She meets a Wolverine fan dressed up as him and he tells her that she looks like Jean Grey with the red hair and since she doesn't know who Jean and Wolverine are, he explains that Jean is Wolverine's love and they're a couple. I thought that was very telling of how the movies have influenced public perception.
Alan Davis had an interesting anecdote though which seems to suggest that even in the late 90s, Marvel was still hung up on Logan/Jean as a pairing because they felt it was more popular and would raise sales.
"This was drawn as a joke that I faxed into editorial during the period I was plotting the X-books. I hadn’t sought the writing assignment and only ever intended to fill the role while a new regular writer was found. So I approached the job in a purely professional way as a “short term problem solver” rather than forging a long term plan of my own. There were always lists of characters, events and themes which had to be included in the two main X-books to spin off into the other X-titles. I enjoyed the challenge of pulling the disparate demands together in a, hopefully, cohesive and entertaining story, but there was one “request” that baffled me—a cover image with Wolverine and Jean Grey kissing. My question was always why, what is the story behind it? The answer was always the same, it’s what the fans want and it’s gonna be big—and it will boost sales! I sent my sketch as an alternative that would certainly boost sales."