It seems most reasonable not to give Kirk Intolerence (Klingons) because he did not truly come to hate them until later in his life.
Most people would argue that Sense of Duty (Prime Directive) should be worth negative 10 Character Points. Normally, they would be right. However, Kirk has been known to bend that rule more than once. Also, he clearly values the life of his ship's crew ahead of the Prime Directive. Therefore the negative cost of Sense of Duty (Prime Directive) was reduced to negative 5, but his Sense of Duty (ship and crew) was set to negative 10.
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