I didn't read the resurrection books, so I don't know how they handled it, but, in Generations, Guinan said that part of her remained in the Nexus (and, didn't that part of Guinan have a conversation with Picard inside the Nexus itself?).
Somehow, that piece of Kirk left behind in the Nexus somehow escapes. Perhaps he comes to his senses, realizing again his last, best destiny, and it gives him the strength necessary to remove himself from the paradise. He steps onto the bridge of a civilian vessel chartered by Spock himself, because the Vulcan could feel Jim "tugging at their bond."
Given the strangeness of the Nexus, it certainly is within the realm of possibility that Kirk is "resurrected" in this way. Of course, it would be a complete surprise to everyone in the Federation -- especially those who have seen the gravesite on Veridian III.
With a renewed lease on life, I could see him using his legendary status to get up to speed on modern technology, get a command, and get back out into space. Who knows, maybe he even finds a way to get Picard promoted and get the Enterprise for himself!
On killing him, I think the way things were presented in Generations was fine. I don't think it was necessary to kill him at all, to be honest; it didn't really add to the story. I think Kirk is the type of character who, despite his attempts at suicide by heroics, would somehow survive everything and face the one obstacle he truly fears...old age. I think he'd become some form of mercenary adventurer, just for the adrenaline rush, and do that until his body just couldn't perform anymore.
Then, I could see him find some nice ocean on an out-of-the-way planet, and live on a sailing ship, alone, until either time or the sea claimed him. Not heroic, I know, but heroics alone couldn't kill him...he's tried, you know.
Davy Jones
"Frightened? My dear, you are looking at a man who has laughed in the face of death, sneered at doom, and chuckled at catastrophe! I was petrified."
-- The Wizard of Oz