Agreed. The change in tone doesn't quite work. I guess they needed to kill off poor Yeoman Paperweight at the beginning to establish the Kelvans as a credible threat, but the happy, smiling finale is at odds with the callousness of her execution at the beginning of the show.
Kirk could have still made peace with the Kelvans at the end, in the best STAR TREK tradition, but they didn't have to be so chummy. It would have better if the peace had been a bit more of a strained, wary affair--like with Khan at the end of "Space Seed."