That reminded me of an unfinished project of mine, aiming to completely remake AOTC, which featured a new origin story for the clone army as well as some other drastically changes and restructures.
The idea was basically to change the kaminoans original client from the republic to the trade federation.
The story goes like this: After TPM Nute Gunray turned to Silo Dyas (possibly Dooku’s underling, hadn’t worked out his story) to acquire a clone army, because the droids have proven themself inefficient in combat.
However Obi-Wan discovers this operation during the events of AOTC and after he informs the Jedi and the senate of this army, they decide to bust the deal and payed the Kaminoans twice of whatever Gunray offered them. Venal as the Kaminoans are (luckily this is set up by Dex) they agree and the republic acquires the service of the clones.
Here is the scene of Obi-Wan informing the Jedi and the Chancellor:
Now on to Order 66. The existence of this protocol doesn’t make sense, if the clones were never intended to fight side by side with the Jedi. To be honest I don’t have a perfect solution to explain why it exist, so sadly it’ll remain as a deus ex machina to get rid of the Jedi for the OT to happen.
Maybe Palpatine planed all this or maybe the protocol was intended to keep the Clones from revolting. Any explanation is as bad as it being a safeguard against rouge Jedi, which only Tyrannus and the Kaminoans know of.