I'm not sure what more we could have seen in the denouement of this novel about Starfleet Intelligence. There will be repercussions for Pike, but the main thing is that the cloaking specs did not make it back to SI.
I honestly did not notice any of the deviations from the Prime continuity. The characters of Pike, Boyce, Number One, and Spock were written well and felt like the same people from "The Cage" a little earlier in their careers. I especially like the way the book ends with a twist on a classic moment from that pilot.
The book itself is riveting. Each of the plotlines is interesting, and they blend together sweetly by the end. I would agree with the poster who gave this a 4/5, although it's an 8/10 on my scale. It is worthy of being read more than once.
One of my only complaints is the Russian captain. I get that we were supposed to hear the stereotypical Russian accent in his dialogue, but the frequent word-dropping did not seem in character for such an intelligent man. I would expect him to either speak in complete sentences in English or speak Russian with the UT activated.