For one, Obi-Wan in AOTC only hears the name "Tyranus", with no indication that this person is a Sith. Sure, it sounds like an "evil" name to our ears - but in general, and especially in a vast, pluralistic society such as the Republic, comprising many different cultures and races, you really wouldn't be able to judge someone's character by the presumed evilness ( or lack thereof ) of the sound of their name. I mean, you don't get to pick your name. Well, some people do, but you know what I mean. For all we know the kindergarten classrooms on Coruscant are filled with little Tyranuses.
In what is now Legends-canon, circa 2005, Yoda believed Tyranus to have been on the side of the Republic:
"By someone on the side of the Republic, chosen he was on Bogg Four to be the clone template." ( Yoda, Labyrinth of Evil )
Also, from the Jedi POV, Sifo-Dyas - one of their own - might have been involved in the creation of the army, or at least in making the initial contact with Kamino and placing an order. That this would have to have been done in "rogue" fashion is certainly significant, but we have precedent in Qui-Gon for Jedi sometimes acting independently of the Council or going against the Council's wishes. It's not unheard of. And for all we know Sifo-Dyas might have done something like this before, in response to Force visions or whatever other reason. Certainly the Jedi in AOTC seem doubtful but it is important to remember that Sifo's involvement is never disproven during the film, Obi-Wan's impressions notwithstanding.
Going back to Labyrinth of Evil, it was revealed in that text that Yoda returned to Kamino and found apparent evidence of Sifo's involvement:
Obi-Wan turned to face Yoda. "Master, did Sifo-Dyas order the clone army?"
Yoda nodded. "Contacted the Kaminoans, he did."
"Without your knowledge?"
"Without it, yes. But exists, a record of his initial contact."
( Labyrinth of Evil )
By the time the Jedi learned of the existence of this army, they needed it. The clones came to the rescue of many high-ranking Jedi on Geonosis and thus hardly looked like a threat to the Jedi at the time.
[ Of course, as is its wont, The Clone Wars made the situation significantly more problematical, by revealing to the pre-ROTS Jedi that Tyranus was Dooku, that Dooku was involved in the creation of the clones, and that the clones had a secret implanted chip prone to potential malfunction! Not to mention Yoda getting a vision that showed clones attacking Jedi! SMH. ]