It must be something like this.
It would be absolutly idiotic of Palpatine just to order the clones to kill the Jedi.
That would cause hundrets of Riots, because the Jedi are feared and respected throughout the galaxy.
His methods are more subtile, just like the creation of the Sepratists movement.
Because it is somehow, HIS clone army he could start of his own putsch against the defendless Republic and gain power.
But he wanted the people behind him. And that's exactly what he needs to wipe out the Jedi.
Palpatine is too clever. I don't think we will see some kind of putsch in Ep3. He just transforms the Republic into the Empire. Just the same way Hitler did it.
To appear legal, is the main part of their strategy.
Everything else would set up a rebellion too early.
So my question was: How do Palpatine manage, that the public believes the Jedi are dangerous.
So far I like Jedi-Monks Idea with the mindtrick.