Elizabeth III is not an irrational nut-job
You know, I've said this before and I'll say it again, Elizabeth is not the irrational nut-job some people think she is. She didn't exactly reach the conclusions she reached about who was responsible for the assassination of her ambassador and the near-assassination of her neice in a vacuum, you know. The readers know a heck of a lot that she doesn't, and while Honor may not agree with all of her conclusions, Honor is (1) aware that Elizabeth (and Grantville) have to make the final calls and (2) that her own perspective predisposes her in certain directions, just as Elizabeth is predisposed in her own directions. Even if Honor discovers that every one of her own suspicions about who might have been responsible for the assassination atempts (other than the RofH) were justified, she is scarcely likely to "slap Elizabeth silly" for McKeon's death or anyone else's. For one thing, she knows that know one in the universe is going to be more wracked with guilt over having been wrong than Elizabeth Winton and she knows that Elizabeth would have been just as wracked with guilt if their positions were reversed. There are times I almost regret having made Elizabeth a fallible human being with the sort of strong personality which can also have strong flaws, since people seem to have fastened on the flaws without particularly noting the strengths. No, she isn't perfect and her judgment can sometimes be affected by her personal feelings. She is, however, aware of this and tries (not always successfully) to compensate for it. She has also been responsible for guiding her outnumbered star nation through twenty-odd years of fighting for its life and, overall, done a pretty fair job, I think (the SEM is still here, after all). As I've said before, she -- like Honor -- has the weaknesses of her strength, and Honor is very well aware of that. It colors her attitude towards Elizabeth in many ways, but Honor (for one) doesn't think she's a dangerous nut and Honor knows her better than most, wouldn't you say? The fact that they don't always agree and that they remain so close despite that fact actually says a great deal about the strength of personality both of them possess, I'd say.