Star Trek: Everything We NOW Know About The Lost Era

Tuvok, it was established in Star Trek: Voyager, left Starfleet for several decades, early in his career. Until the revelations in Star Trek: Khan, the only reason the audience had been given was Tuvok's discomfort around humans in general.

Flashback depicts one of his earliest missions aboard the USS Excelsior, roughly two months out from Starfleet Academy. Despite trying to make a good impression on Captain Sulu with tea, he was not opposed to voicing his opposition to his commander's violation of orders. He had also previously vocally opposed the Federation's peace talks with the Klingon Empire. 

Khan depicts Tuvok in the months following the launch of the Enterprise-B. He was still serving aboard the Excelsior and was assigned to surveil Dr Rosalind Lear. This raises an ethical dilemma for the young Vulcan. Lear's discovery of the Augments' conditions post-exile, as well as the revelation that she herself is the daughter of Khan Noonien Singh, broadens Tuvok's understanding of humanity. Despite Captain Sulu's resentment toward Khan and the Augments, Tuvok vows to fight for their rights in his career going forward. 

With this context, it can now be surmised that the reason for his departure from Starfleet was, at least in part, due to the conflict he must surely have encountered in his search for equal rights for Augments. Though this affects only a single Vulcan, it also presents the late-23rd and early-24th Centuries as still being unkind times for Augments to live through.