I don’t think the Jedi knew that Dooku ordered the clones. Obi-Wan was informed that a Jedi named “Sifo-Diyas” had ordered the clone army. (We’re told he was a member of the Jedi Council ten years before, although we never saw him in Phantom Menace.)
Later, Obi-Wan confronts Jango on who ordered the clone army. He respons, “Sifo-who? I was contacted by a man named Tyranus on one of the moons of Bogden.”
Dooku is never addressed by anyone as “Darth Tyranus” except by Sidious at the end of the film. Although “Tyranus” is apparently Dooku’s Sith title, it’s not common knowledge…indeed, despite the red lightsaber and use of the dark side, nobody seems to know that Dooku IS a Sith. Note his speech to the captive Obi-Wan…“Join me, and together we can find the ring–er, I mean, destroy the Sith!” Dooku implies that he knows what the Sith are up to, but distracts from the fact that he is one. (Note that Dooku’s offer to Obi-Wan closely matches Vader’s offer to Luke at the end of Empire: it basically translates as “Help me become the new Dark Lord, and you can have my old job.”)
My theory: Yoda and Mace ordered the Clone army. Note the funny look that passes between Yoda and Mace when Obi-Wan contacts them. Note also that Mace mentions that the Jedi are losing their ability to use the force–that the Jedi are, in fact, becoming defunct. (I have theories on why this is happening, too.) My suspicion is that when this first started happening, Mace and Yoda decided to take confidance in the only person they thought they could trust…bum bum bum…newly-elected Supreme Chancellor Palpatine. It would have happened something like this:
Yoda: “Supreme Chancellor…speak with you, we must. Grave matter, it is.”
Palpatine: "Master Yoda, Windu. Of course.:
Mace: “The Jedi’s ability to use the force is mysteriously diminishing. We fear that within the next decade, we will be unable to protect the Republic further.”
Palpatine: (Inwardly chuckling) “That…would be a terrible tragedy. I have a solution. I know of this planet, Kamino…what if we cloned an army of warriors to fight in the stead of the Jedi?”
Yoda: “Like this, I do not. Deceptive it is.”
Palpatine: “Perhaps…but consider the panic that would ensue if people knew that the Jedi were failing…”
And whammo…Palpatine gets an unstoppable army ready to take the place of the Jedi in their hour of weakness.
I also suspect that Yoda’s line in Jedi, “Don’t underestimate the power of the Emperor,” has something to do with this. Basically, that Yoda was ALSO suckered by Palpatine, and he wants Luke to be aware of it.