1) Though Travis had strong Space Boomer roots, he was also not afraid to stand against them in favor of starfleet and to tell the old-schoolers that times were changing and they should embrace it. In both the episodes where Travis faced an old warp 3 (I think) freighter, he tended to stand against them rather than for them. Archer made a tough call in the Maru affair and Travis saw the entire event unfold; I just can't see him completely turning his back on his CO after all they had been through together and Travis KNOWING it was a no win schenario. Travis was well aware that he owed Archer HIS life on many occasions.
Owing someone your life doesn't mean you need to always be willing to go to bat for them, especially if they've done something you find yourself having a great deal of trouble forgiving. I think what we saw was Archer finally doing something that pushed Travis's sense of morality too far.
Maybe he did witness a no-win scenario, but it's not like endless numbers of fans haven't said, "I'd at least try doing this rather than just giving up." And those fans had a lot less invested in the situation than Travis did.
From where he was sitting it probably felt a great deal as though Archer was turning his back on the Horizon as well...if it had been the Horizon instead, Archer would not have behaved differently (Disclaimer - I haven't read KM in awhile).
Anyway, there's a difference between believing someone behaved improperly and believing they behaved in a manner that will prevent you from being able to work well with them going forward.
As to the main topic, I didn't speed through these books as I did through, say, Destiny, but that by no means doesn't mean I didn't enjoy them. I didn't find them a struggle, but the RW books have to paint an even greater tapestry than Destiny, as they're showing us the Romulan side and the perspectives of people who are watching from the sidelines. To take any of that away would be to simplify the story and would, to my mind, be detrimental. Of course, that also means that some of the stories will prove less captivating than others, especially if you're reading about charactes who really don't have any significance to the greater arc.
We all know that during the Dominion War DS9 couldn't really have been at the forefront of every major situation that occurred, but we accept (for the most part) what we got because you couldn't expect the series to start hopping around the galaxy showing events unrelated to the main characters. I consider it a strength of the novels that they aren't inhibited in the same manner.