I don't buy that Sarek married Amanda because he knocked her up. For them to produce a child would (IMO) have required far more medical intervention than simply forgetting about birth control. Are we forgetting about copper-based blood versus iron-based blood? And that is just for starters. It is amazing enough that Humans and Vulcans are so sexually compatible despite their differances, without deciding that they can successfully interbreed without a heckuva lot of outside help.
I believe "It was the logical thing to do...
" was partly humour on Sarek's part (especially
given where / when / how this line is used). Yes, we have seen several Vulcans who have displayed a sense of humour - that is why they make such great straight men. Mostly, though, it was (IMO) Sarek's way of saying that personal feelings (they loved each other) dive-tailed very nicely with The Big Picture (encouraging Humans and Vulcans to get along).
Regarding Commodore Stone. Not a lot I have to say here. His "offer" to Kirk may seem odious to some, but it wasn't like he was calling for facts to be changed. If Jim Kirk had stepped up, admitted his guilt and taken what was coming (loss of command, etc.), then a messy expensive (in manpower, anyhow) trial and (more than likely) a load of paperwork would be avoided.
Plus, Commodore Stone probably (at that very early stage) saw the offence as errors in judgement and/or some kind of aberration on Jim Kirk's part, rather than as deliberate murder. He was a brilliant officer, and no good would have been served (to the deceased, Star Fleet, the Federation or Kirk himself) by nailing him to a cross (so to speak). Kirk (as far as could be determined) had clearly done The Wrong Thing, or a couple of same, and had to account for that - but that did not equate with going all 'Old Testament' and destroying him completely.
One sees this happen in trials, and for good reason. Admit your guilt, and it takes the onus off the court trying to prove whether or not you did the deed. The punishment is usually more lenient (even if only slightly) in such cases.