They knew that Dooku was a Sith Lord and that the mysterious second Sith was called Darth Sidious.

They were actively working on uncovering the identity of this Darth Sidious when Anakin said Palpatine was a Sith Lord, specifically the one they had been looking for.

They knew he and Dooku had conspired to start the Clone Wars, and that Dooku had placed the order for the Clone army, but the Order 66 protocol blindsided them.

Also, Sidious used an audio device to record the ”assassination” putting up an act of a defenseless old man.

Source?

Novel of Revenge of the Sith

That’s not canon anymore.

It's a complicated one to say the least.

Moose is right in that there's no moral equivalency between the Sith and the Jedi. They're both Force users with lightsabers but that's where most of the similarities end; the Sith are a dangerous group hellbent on destroying the Jedi. With solid evidence, I doubt there would be much issue with a lawful arrest carried out by proper law enforcement.

That said however, the Jedi who moved to arrest Palpatine all held military rank. This complicates things in that Palpatine was an elected official who was in office due to a lawful use of his constitutionally-conferred emergency powers. An arrest of this manner could justifiably be called a coup d'etat, considering that it was the aim of the Jedi to affect political change through a unilateral use of force.

In this context, Palpatine's violent response to the Jedi would be an entirely legitimate act of self defence. We can look at this from two angles; firstly, in accepting the Jedi are a rogue attacking force, Palpatine would in effect be the military Commander-in-Chief defending against an opposing and attacking military force. No issue here. We could alternatively look at it as Moose did, with four police officers surrounding a suspect.

In the real world (and please don't take this as legal advice), where a police officer draws a weapon on a person where there is no solid evidence that a crime has been committed, and the other person genuinely believes that they are about to die, it would be arguable that for the suspect to then shoot the officer would be a legitimate act of self defence.

In this case, the simple "Oh well my mate who's also a part of my religious gathering told me he was guilty of being a part of another religious gathering" would likely not meet the evidence requirement for such a use of arms, in some countries. Don't shoot police officers, kids.

I think this comes down to the simple idea that sometimes it's okay to break the law for the right reasons. It's the idea that all revolutions, coups and riots in history have been built on; it's not as simple as legal = good / illegal = bad. Were the Jedi right? Yes. Does that mean that it's wrong to suggest they were acting illegally? Not at all.

Hope that helps, @Moose05

Interesting. The quasi-religious and military nature of the Jedi in the Clone Wars does indeed complicate things.

I wouldn’t be surprised to learn that Chancellor himself encouraged the Jedi to take on military roles for the explicit purpose of being able to take this defense.

It's certainly a credible idea. Order 66 was programmed into the Clones from day 1 afterall.

It's worth pointing out that public opinion was dead against the Jedi coming up to the end of the war - per Dave Filoni's TCW commentary and the protests outside the temple in the Ahsoka arc of Series 5. I think that, even had Palpatine not directly ordered Order 66 to be executed, there would have come a point at which the public would have demanded that the Jedi be excised from the Republic by any means. That would ultimately lead to the same result come what may.

There was no proof that he organized the entire clone wars for example. So he just told the people that he was unjustifiedly attacked in his office. That's how people kept supporting him.

I think there was probably quite a lot of proof, the only issue is that the Jedi didn't bother to collect it.

That could be because the Republic, like the US, doesn't allow a sitting premier to be prosecuted. Alternatively, it could be that Mace Windu thinks he's a cowboy. Ultimately, we don't know either way.