On some level this answer does have a certain ring of truth to it.

Kirk had just been involved in 'saving' the Khitomer conference. The Federation was heading towards a brave shiny new future with the Klingons but Kirk was in many ways a product of war, trained to suspect the worst of Klingons even if his instincts were to welcome the new era with an open heart and befriend them. Captain Ben Maxwell (TNG: The Wounded) is what we get when somebody resists the new broom. Maybe Kirk feared he could be like that.
Or perhaps Kirk retired because he simply recognised that his page in history was done, and that the next generation needed to be able to forge a fresh path without "dinosaurs" like him.