I too want to know how, if at all, are we able to have Imperial Intelligence reinstated. I ended up with a similar ending to many here where I was mostly grey, dipping from time to time to Light 1 but finishing as Dark 1 and Intelligence was dissolved but I chose all of the "Stay loyal to the Empire" options. I chose not to turn over the Codex to Keeper because even though I liked him from start to finish and respected him highly, the storyline (and my own personal inclinations) forced my Sniper to trust no one but herself (perhaps to go on a killing spree of every single person on that list)

My Sniper loves the Empire and believes in what it stands for, but will take still being able to serve, albeit from the outside, over being a puppet to the Sith who care more about power than the betterment of the Empire. My only hope is that my Sniper will be waiting in the wings ready to swoop in and save the day, kill the conspirators, reinstate Keeper/Minister of Intelligence, and reestablish Imperial Intelligence in some kind of future content.

One interesting thought: in a meta Star Wars story sense, perhaps the most canon ending is the dissolution of Imperial Intelligence, the creation of Sith Intelligence as a corrupt organization and the eventual [canon] collapse of this Empire all stemming from the SIth dissolving the only organization capable of saving the Empire!