One good reason to do ships in parts would be economy: if something goes wrong with one part (say, every 1,234,567th atom is of the wrong sort), you ditch/dereplicate just that one, rather than the entire ship complete with the potted plants.
So let's assume that Starfleet sent Kirk on this mission to try to intentionally get him killed (which is already a preposterous scenario, but I'm willing to play devil's advocate here.)
Well, having him humiliated is a more realistic goal, and certainly achievable in the context.
Admiral Bob specifically wants Kirk to lead the mission, and Kirk states that his ship is not up to the task. So...why didn't either Bob or Kirk suggest just having Kirk transfer to a ship that was better suited to the task?
This would simply presume that Kirk is resigned to his fate already: whenever Bob shows up, it's another attempt to discredit Jim, and Starfleet is just being extra sadistic by using Jim's supposed friend as the messenger. Any attempt at trying to be rational about it would simply mean more trouble for poor Bob.
This double jeopardy would be required to explain away the smiles as sad ones. The rest would then click in place easily enough.
First of all, it wasn't Starfleet's idea to send Kirk on the mission; it was Spock's, without Kirk's knowledge. And second, the conspirators' intent was to prevent the peace treaty, not to specifically make Kirk a patsy. If Starfleet had instead chosen, say, the aforementioned Captain Styles for the mission, then it would have been Styles and his ship that would have been framed, not Kirk.
This assuming that there was something unexpected about Spock choosing Kirk; or that there was free will involved in any fashion.
Spock
vouched for Kirk, and quoted the Nixon platitude. Doesn't mean (or sound like) Spock
chose Kirk - he merely okayed somebody else's secretly malicious choice, a choice presumably facing opposition before Spock did the vouching. And the choice probably did not need Spock's okay anyway, but it made the conspirators do the "Exxxxxellent!" finger-spire-gesture when it did transpire.
And yet he also saved Earth, and presumably, the families of all those Starfleet commanders. So I don't see Starfleet being too pissed off at him.
It would be a balance issue, yes. All we need is pissed enough.
Timo Saloniemi