The following is the recount of the Hundred Year Darkness, the reason behind the Dark Jedi Exile from the Galaxy, and the initial cause for the formation of the Sith Empire.

The Hundred-Year Darkness , also known as Second Great Schism, was a conflict that began in 7,003 BBY, and lasted until approximately 6,900 BBY. A group of Dark Jedi created monstrous armies to battle the Jedi Order and the Galactic Republic. After decades of fighting, the Dark Jedi lost the war in the final Battle of Corbos.

The Second Great Schism began when a small sect of Jedi Knights began practicing extended uses of the Force. By relying more and more upon the Force, these Knights learned that using the Force of sufficient intensity could bend life itself. With their new powers, the Knights experimented upon other life forms to create new species and predators as extensions of their will. It was postulated that their power could even be used to end death and revive dead worlds. Other Jedi looked upon these new powers with suspicion, suspecting that such power would only lead to abuse. The earliest rebels, the Legions of Lettow, had been defeated in the First Great Schism, but their legacy remained, and a second group of dissidents would emerge, led by such rogue Jedi as Ajunta Pall, XoXaan and Karness Muur.

All great conflicts begin with passion, and this one was no different. Firmly adamant in protecting their newly-acquired powers, this sect of Jedi sought to convince the other Jedi to join their quest for eternal life and galactic bliss. The others were not convinced, and tried to distance themselves from the situation. Firmly convinced that their way was right, the arguments turned into conflict. The rogue Jedi were exiled along with their teachings. A war had begun that would last a hundred years.

The War

Retreating from Jedi worlds such as Tython, the exiled Jedi raised an animalistic army of dark side abominations. The first form of Korriban zombies would be created during the earliest stages of the war. However, even against these incarnations of the dark side, the Jedi began to push the rogue Jedi back. The animalistic army was easily overwhelmed by the power of the Jedi, but the exiled Jedi refused to surrender. Duels to the death between Jedi became the end of many battles.

By the second half of the war, the Dark Jedi were in a state of despair. They were simply outnumbered, and could see no way of winning. However, the Dark Jedi refused to surrender, and pooled all their resources into creating the most fearsome dark side creatures ever seen. Supported by monstrous creatures, such as the Leviathan, the Dark Jedi armies were reinvigorated. Armies fled in terror from the abilities of the Leviathan to suck life essences into the blister-traps upon their backs.

However, under combined efforts from the Jedi, the Exiles were continually pushed back. The last stand of the Dark Jedi was on the world of Corbos. Infighting, along with the bombardment of the Jedi and the Republic, led to the surrender of the last of the Dark Jedi.

The Exile

After their defeat on Corbos, the surviving Dark Jedi were rounded up by the Republic armies. Stripped of weapons and armor, the Dark Jedi were at the mercy of the justice of the Republic. Although members of the Republic wanted public executions, the Jedi leaders were inclined to banish the rogue Jedi into the unknown, in the hopes that, with time, they would see the error of their ways. On the plains of a barren world, the Exiles, as they became known within the Republic, were herded onto unarmed transport ships. Several fighters accompanied the ships to ensure the departure of the Dark Jedi from Republic space. The Hundred Year Darkness was over, and the Jedi had weathered the Second Great Schism.

The above portion of this article was unedited and taken from Wookieepediea.

In the early days of the Jedi, a great schism tore the order apart. Jedi who had tapped the forbidden power of the Force's dark side rebelled against their light-sided brothers. After a terrible war, the Dark Jedi were exiled from the Republic. Past the Republic's growing borders, these castaways discovered Korriban and the Sith people.

The Above was taken unedited from StarWars.com

From the Sith Perspective, I can see where they might believe that the Jedi attempted to wipe them out completely, however, we know from the movies that they will say what the think will get them what they want. From the above account, you can clearly see the Jedi’s Reasoning for exiling the Dark Jedi… The Republic was calling for executions, the Jedi on the other hand, allowed the Dark Jedi to live, essentially saying that if you will not come back to the light side, than don’t practice your dark side teachings here.

The Jedi very easily could have killed the Dark Jedi on sight, but they chose not to. The Jedi were merciful where the Republic would not have been, After a hundred year war started by the Dark Jedi and their creations, the Jedi were still hopeful that a peace could be found eventually. Did the Jedi Commit Genocide on the Dark Jedi? Absolutely not. The Dark Jedi started a War, and were exiled for it, in no way does that constitute Genocide, and the idea that the Jedi were hoping they would Die in the Unknown regions, knowing full well the power that they could harness is far from substantiated in established lore, more likely that the Jedi would hope that they would return and agree to come back peacefully.