Another possible solution (in a completely different direction) would be to play off the aftermath of the Temple bombing that's either this year or next year. Remember: unless we change things, then Bariss Offee will set off a bomb in the Jedi Temple, and Ahsoka Tano will be framed for it. The Jedi Council will (predictably) be horrible and decide to evict her from the Jedi Order before the trial, while the trial itself gets railroaded by Admiral Tarkin of all people. Basically, everyone is against her except Anakin 'Skyguy' and her 'friendly' rival Asajj Ventress. (That's canon. In this universe, she'll probably have us as well, which is probably our best shot of recruiting her and/or Anakin Skywalker away from the Jedi Order...).
Anyway, my idea was to pull some strings with the Senate, and try to ensure that the Jedi Council's response becomes generalized. That is, if someone in a position of command in the GAR is suspected of treasonous activity, then they are automatically suspended from that position until an investigation takes place. Given the connection to Ahsoka, this would be an obvious anti-Jedi measure, at least for Jedi who are serving as GAR generals.
However, it wouldn't be exclusive to generals. Specifically, this new law would apply to anyone in the chain of command, up to and including the top of the chain of command. If the Supreme Chancellor is suspected of treason, then by this rule he would be automatically suspended from the position of Supreme Chancellor.
At that point, all that's left would be to have the Jedi publicize the fact that they believe that a Sith Lord was responsible for starting the war, and that the Sith Lord has ties to both the CIS and the Republic. Vague, generic, almost entirely useless info... except for one implication.
A Sith Lord would try to attack & eradicate the Jedi Order.
If the Supreme Chancellor gives the order to eradicate the Jedi Order, he may have fallen under the sway of the Sith Lord.
If the Supreme Chancellor fell under the sway of the Sith Lord, he is acting against the interests of the Republic and should be suspected of treason.
The Supreme Chancellor might not be the Supreme Chancellor as a result of giving those orders.
The wording of Order 66 makes the 'verified as coming from the Supreme Chancellor' into a formality (again, a hologram was the only verification needed). But if the mere fact of giving such an order throws that verification into doubt, then the logic circuit of the inhibitor chip would not force immediate compliance.