There are no on-screen references to Kirk's death after Generations. He is generally mentioned a few times, but nothing about his death.
Nothing in the post-Generations canon would be disturbed by showing that one of the many loopholes in the film (or any of a dozen other ways) was later used to revive Kirk/ retrieve him from the Nexus etc.
I always saw Generations as the then current regime's way of burying TOS as they went on to launch what they hoped would be an even more successful series of TNG films. Didn't work out that way.
Shatner as Kirk would generate a lot of media attention and interest from the general public. If the film has a good story, it would be an additional boost to help it succeed. Seems to me if the only thing standing in the way of that is 30 seconds in a 13 year old film, never referred to again, you could find a way around it, if it fits their story.
If Nimoy is in it as Spock, it will be disappointing that Shatner did not get in at as well for once last appearance as Kirk.