1. While the Imperial Remnant maintained many of the trappings of Palpatine's regime -- a strong military and limited venues of public expression -- it was far more progressive and devoid of the rampant injustices found during the height of the Empire's power. Slavery was abolished, as were the extremes of anti-alien sentiment. The Imperial Remnant unobtrusively continued adhering to the strict tenets of the New Order, growing increasingly irrelevant to galactic affairs.Decades after the disastrous Battle of Endor, our saviour finally arose from the ashes of the Empire. He bore the noble bloodline of Vader and the dark power of the Sith. It was under his leadership that the Empire was reborn. It is under his leadership that we shall accomplish the unprecedented: the conquest of a new galaxy. A galaxy bereft of strong leadership. The galaxy of Star Trek!
The Empire is a fair place and is controlled by Gilad Pellaeon, who had made peace with the Republic.
2. During the Yuuzhan Vong invasion, Pellaeon recognized the threat the alien menace posed, even though their incursion had skirted past Imperial space. Despite some protest from the Moff Council, Pellaeon committed his forces to a joint Imperial-New Republic offensive at the Battles of Garqi and Ithor. Despite the best efforts of Pellaeon and New Republic Admiral Traest Kre'fey, the Yuuzhan Vong destroyed the ecology of Ithor. Shocked by the power of the attack, the Imperial Remnant recalled their assistance of the New Republic, and chose instead to sit out the invasion on the sidelines.
The YZV are killing the Republic and the Empire even tried to help. They could not put up forces to help the Republic after the defeat or even invade the ST Galaxy without being vulnerable to attack.
3. It was a move the Moff Council would come to regret. They falsely believed the Imperial Remnant safe from attack, since it had been ignored for much of the invasion. The Yuuzhan Vong proved that assumption wrong, when it brutally attacked the Imperial worlds. Pellaeon was critically wounded in the attack, but the sudden arrival of a Jedi mission exploring the Unknown Regions saved his life. Jedi healers stabilized Pellaeon's condition, and Luke Skywalker and Jacen Solo helped Pellaeon expose infiltrators in the Imperial ranks and refocus Imperial efforts to assist the newly founded Galactic Federation of Free Alliances.
This proves that the Empire could not attack ST because of the YZV. In fact the Republic and the Empire are forming the Galactic Federation of Free Alliances. This only makes them more friendly to other empires.
4. I assume that the character Kanos in this story is the Imperial Royal Guard, Kir Kanos, who has tried to keep Palpatine's dream alive. He was stopped and is now Kenix Kil, and posed as a bounty hunter. With this alias, he was better able to hide from the hunters pursuing him. Kanos succeeded in killing would-be Emperor Xandel Carivus. Kanos' current whereabouts are not known. There is no way he could have a SSD or DS in this invasion of the Federation.
Conlusion: With so much shit going down in the SW universe, the Empire has no Forces or Will to attack and invade ST. This makes it easier for ST and SW to get along more. If anything, a Fanfic should be based on the ST and SW universes joining up to fight the Yuuzhan Vong.
Plus Palpatine kept dying and coming back, whose to say that Anakin's spirit didn't move into a clone body after death and return to subjigate the Empire. 
