Facts change over time of course. 
However...
There's a comic book miniseries all about Vader hunting the remaining Jedi across the Galaxy after after order 66 was given, and a few had slipped through the cracks.
http://www.goodreads.com/book/show/17372081-star-wars
In the new cartoon, a minor Sith working for the Emperor turned the skeleton of a dead Jedi into a force-radio that transmitted a frightened distress call to any nearby Jedi who would quickly die if they responded to said distress call.
Palpatine knew who the Jedi were because he controlled the war and deployed them were he sought fit, with order 66 the dark lord killed the Jedi he could with efficiency, counted the bodies and and made a list. He knew who was missing because like Santa he checked his list twice, and then did something about it.
This is a question of religious freedom.
The Jedi would not tolerate a Sith, and he would not tolerate the Jedi.
No quarter would be given.
I do wonder what would have happened if Palpatine volunteered that he was Sith without admitting that he was Sideous or that he had done anything wrong, evil, or criminal?
Which actually might have been what happened?
Did he say "Yoohoo, I'm 5 minutes from killing everyone?"
Nope.
He revealed himself voluntarily.
And they tried to arrest him.
Heads rolled.
He was the elected Chancellor, they didn't have the legal right to do jack shit.
Unless its republican law that all Sith must die.
So everything he did was self-defence?

However...
There's a comic book miniseries all about Vader hunting the remaining Jedi across the Galaxy after after order 66 was given, and a few had slipped through the cracks.
http://www.goodreads.com/book/show/17372081-star-wars
In the new cartoon, a minor Sith working for the Emperor turned the skeleton of a dead Jedi into a force-radio that transmitted a frightened distress call to any nearby Jedi who would quickly die if they responded to said distress call.
Palpatine knew who the Jedi were because he controlled the war and deployed them were he sought fit, with order 66 the dark lord killed the Jedi he could with efficiency, counted the bodies and and made a list. He knew who was missing because like Santa he checked his list twice, and then did something about it.
This is a question of religious freedom.
The Jedi would not tolerate a Sith, and he would not tolerate the Jedi.
No quarter would be given.
I do wonder what would have happened if Palpatine volunteered that he was Sith without admitting that he was Sideous or that he had done anything wrong, evil, or criminal?
Which actually might have been what happened?
Did he say "Yoohoo, I'm 5 minutes from killing everyone?"
Nope.
He revealed himself voluntarily.
And they tried to arrest him.
Heads rolled.
He was the elected Chancellor, they didn't have the legal right to do jack shit.
Unless its republican law that all Sith must die.
So everything he did was self-defence?