With regards to Kirk's bigotry against Klingons in Star Trek VI
and the idea that it is inconsistent with his earlier characterization, I would like to offer this for thought:
My paternal grandfather, who was white, died when my father was only 11 years old, so I never knew him. But I've grown up hearing stories from my father and paternal grandmother about him -- and something in particular about their stories always intrigued me. It seems that my grandfather, who was a truck driver, had, as was common in those days (1960s), a number of close male friends. They would hang out all day on their days off, working on cars, drinking beer, shooting the breeze, etc.
Most of his friends were white -- but one man among his associates was black. He had a nearly identical relationship with him; they would hang out, talk, work on car engines together for fun. My father and grandmother both describe their relationship as being virtually identical to those with his white friends. And yet, when the sun set at the end of the day, my paternal grandfather would not do as he did for his white friends and invite his black -- friend? associate? -- over for dinner. Nor would this other man invite him over to his house. There was a boundary between them that prevented from from becoming closer friends as they would have with men of their own skin color -- even though, say my grandmother and father, their relationship was up to that point nearly identical with those of other friends.
And when the evening came and this other man had left, my paternal grandfather would often watching the news with my grandmother and father -- and upon seeing a news piece about a white person being attacked by a black man, or about the civil rights movement, or about any crime allegedly committed by a black person, or about a black person at all, my grandfather would often become agitated, use the N-word, and talk about about how black people were ruining the country and could not be trusted.
His having died when I would have been -11 years old, I never met my paternal grandfather. But that story, of the seemingly contradictory behavior -- the man who could be almost-friends with a black man one minute and a raging racist the next -- has always stayed with me. It has often suggested to me that people can harbor prejudices and racial animosities in the same breath that they may try to be friendly and polite, that their behavior can be essentially inconsistent and self-contradictory.
So somehow, the idea that James T. Kirk could believe that prejudice against Klingons as a species is wrong, could work for many years to fight that prejudice in himself, could try to find a way to build bridges of trust and make diplomatic overtures -- and yet find himself blaming their race for the death of his son, and find himself feeling so utterly bitter and threatened at the thought of a fundamental change in the relationship between the Federation and the Empire, at the thought of a peaceful alliance, that he would behave as he did in Star Trek VI
... this idea has never bothered me. I can completely accept the idea that James T. Kirk encompasses both of these self-contradictory impulses, and that at his best he's fought his own prejudices -- and that at his worst, he's sometimes given into them.
Just my food for thought, inspired by stories I've heard within my own family. Your mileage my vary.