How to handle the Jedi's fall

This is the basic rundown on my version of the Great Jedi Purge:

In the decades following the end of the Third Clone War, the Empire (in my canon, the Empire had already replaced the Republic prior to Palpatine's rise to power) entered a great depression and corruption spread throughout the Senate.

Palpatine, a young senator at the time, began manipulating his fellow senators -- both the corrupt who wanted to use him to their own ends and the pure who wanted him to return the Empire to its former state of glory -- and used them to work his way up the hierarchal ladder until he was elected Supreme Chancellor.

Once in power, he began making a series of reforms which seemed beneficent at the time; the government was reorganized, with many corrupt officials removed from power. As time passed, however, Palpatine's reforms took on a darker edge; the military was granted more control over the general populace and rights were taken away from women and non-humans.

Seeing Palpatine's reformations as a bad omen for the future, many Jedi began to protest against Palpatine and his New Order. However, most of the Jedi of the Coruscanti Order -- the largest Jedi denomination -- remained loyal to Palpatine. Once Palpatine became the new emperor, the Coruscanti Jedi -- who had basically become enforcers of the Empire since the Second Clone War -- became his own personal Army of Jedi.

When the Great Jedi Purge began, it was a small scale, under-the-radar affair; it consisted mainly of Palpatine sending out agents to assassinate the more vocal Jedi dissidents, leaving the rest relatively alone. As he became more corrupt, however, and as the dissenting Jedi became more vocal, the Purge became more public and more violent. In time, entire groups of Jedi protesters were rounded up and imprisoned; some were even killed while in captivity. The Jedi still weren't officially classified as enemies of the Empire -- yet.

It all escalated, however, and in time all Jedi who hadn't pledged allegiance to Palpatine and his New Order were branded enemies of the Empire and targeted for annihilation. Young Jedi children and apprentices were taken from their parents/teachers and sent to reprogramming centres while Jedi academies and training centres throughout the Empire were taken over/closed down/destroyed. Fugitive Jedi relocated to sympathetic worlds which had always held large Jedi populations, hoping that there they would be able to make a stand against the Empire, but the Empire simply sent fleets to bombard those worlds into lifeless rocks.

Finally, after the Jedi had been reduced from billions to millions, Palpatine sent various agents -- Dark Jedi, non-Jedi darksiders, various Imperial agents, and bounty hunters -- to hunt down and wipe the rest of them out. It was in this phase of the Purge that Darth Vader and Boba Fett both made names for themselves.

The Great Jedi Purge spanned five years -- from 18 BBY to 14 BBY -- after which the Jedi -- which had once numbered in the billions, even after many of them had died fighting in the Clone Wars -- were reduced to a mere ten-thousand. These ten-thousand Jedi then went into hiding; some were discovered by the Empire and killed, others simply passed away, while still others became founding members of Luke's new Jedi Order after the fall of Palpatine and the rise of the New Republic.   

I'm actually doing the their fall/metamorphosis in two parts essentially. In the hundreds of years before my prequels begin, the Jedi  for all intents and purposes have dispersed throughout the galaxy. The core motive was moving away from directly working with the senate due to its growing corruption and a belief that they could better serve the citizens of the Republic by offering assistance all throughout the galaxy rather than just the core worlds. 

This would create two side effects. On one hand it allowed them to grow beyond being just knights. Jedi healers, engineers, philosophers, teachers, farmers, now started becoming the rule rather than the exception. Countless users of the force all doing their part to assist without ever using a lightsaber. They had their own first steps into a larger world. 

However this also led to them in many ways becoming mythic rather than public figures. Jedi knights of the past were a highly organized force that were discussed and seen as the guardians of peace and justice that the old days essentially needed. As the centuries went by however and their efforts were put towards more indirect areas, what Jedi were observed seen more exceptional than extraordinary. 

This evolution is at the center of a conflict between Kenobi and the only other active student of Yoda, Nellith, both of who represent the two sides of what the Jedi are to become in light of the Clone Wars. Obi-Wan believes that even though they are already serving in countless support positions, for the sake of winning the war, Jedi need to go back to the old ways and have knights at the front line. To Ben, while he understands their position, the Republic has to come first. 

For Nellith, serving as a quasi-defacto leader of many Jedi, putting them at the front lines offers too many risks. Namely that Knights are the most likely to be tempted by the dark side, and that turning what have been peace time Jedi into soldiers on the frontlines could create enemies worse than what they're fighting. In addition the possible risk of close organization making them easier targets weighs on her mind. There's also a subtext that she has grown to truly value what the Jedi have been allowed to become and doesn't want it to disappear in the fog of war.

In this case both are right. The Republic did need the Jedi at the front to win the war, but that very organization after Episode II will help Palpatine in wiping many of them out and prove Nellith correct. In the end while Kenobi's move wasn't necessarily the wrong one, his failure with Anakin ensured that which helped to save the Republic would serve to doom the both it and the Jedi.  

Ultimately its about expanding the nature and character of the Jedi beyond simple white hats and to further demonstrate what a tragedy their destruction was. It wasn't just the lives lost, but that the new essence of what a Force user could be was annihilated, reducing a vast amount of all kinds of Jedi to much fewer in both kind and number.