Frankly I never found the spy thing believable.
I really didn't think of him as a "spy" at first. More, like, saboteur. In the beginning, he was
accompanied by a *real* spy after all, and he was actually perfect for the mission because an operative without his kind of expertise wouldn't be of much use around experimental warp equipment.
But I do agree that the whole "under cover" thing wasn't a good idea. There were better ways of bringing him back, surely.
The way I would have done it - events in TATV still occur in 2061, but the relaunch only gets there at the end, while all the books take place between Terra Prime and it.
In the end, the final book would have retcond TATV by showing the REAL version of events, in which Trip DOES in fact die, but heroically and meaningfully. Also, the T&T romance continues, but the two are VERY discreet, both being senior officers and all.
Oh, and Trip dies in T'Pol's arms, a MAJOR tear jerking moment, and y'all baww like babies, but you keep re-reading it over and over because it's just THAT beautiful!