It's an interesting question, but as many have pointed out, he's obviously committed to the Vulcan diaspora (as he should, since it keeps the two Spocks relatively separate, but still relevant). I imagine that he'll probably use some of his future insight in a more ambassadorial capacity, for example, accelerating the Romulan unification movement, and perhaps even trying to steer the resulting culture into something that doesn't distrust and hate everything around them, perhaps even joining the Federation at a later date. If he works for the Federation in any official capacity, it would likely be through the Diplomatic Corps, helping the Federation expand while using his timeline's insights to avoid major pitfalls along the way (like, for example, the Klingon/Federation conspiracy from the Undiscovered Country). In this way, the Federation could grow more organically while keeping it's core principles intact without having to resort to moral compromises like Section 31, et al that came up more and more frequently in the 24th century as things got more difficult.
This could have the effect of uniting the Alpha Quadrant well before the Enterprise-D, the Borg, Dominion, etc., making the 24 1/2 century a little less dramatic, but safer and more secure, and all without having to give up a whole bunch of future tech that would probably not really help out in the long run.
As for threats like Khan, The Probe, V'ger, etc:
Khan really wasn't much of a threat, at least to the Federation at large. He certainly was to Kirk personally, but his only danger to the galaxy at large was when he aquired the Genesis device, (something which, honestly, I could see future Spock trying to derail if at all possible, given all the negative repurcussions that resulted from it). But the worst Khan would have done is take over a starship or two, and probably disappear, since it's highly unlikely anyone, even with an advanced intellect like his, could have done anything like take over the Federation, or even Earth in the 23rd century. While arrogant, Khan wasn't stupid. Once he realized the logistics and realities of this era, he probably would have (rather ironically) settled on a world somewhere out in deepest space to build his own empire.
The whale probe... Even extinct, it would be possible to circumvent that disaster. It wouldn't take a whole lot of reveal, future Spock might just sponsor a side project somewhere having Federation scientists studying whalesongs and finding a means of using the Universal Translator to communicate with it. The major problem with the Probe was communication: no one could talk to it, or even know it was trying to talk. If the Federation knew right away it was trying to talk, I imagine the problem would be much simpler. Some clandestine research on the matter would probably work just fine for that.
V'ger might be a bit trickier, though... I'm not sure how to get around that one, exactly, though I'm sure it could be done, too, without spilling the Future bag.