Well look at it this way, Cracken is a Sith, and until he renounces that the Jedi won't trust him. Put yourself in the Council's place, they're already worried the Jedi might be impressionable, what if Cracken got there first?
As to the Truce, it has to be said that it was something of neccessity on the part of the Republic, Cracken had them on the ropes, then relented. In the consolidation afterwards the Republic grabbed several former Imperial Seperatist Worlds so that Cracken's Empire is almost cut in half on a line from Agamar back to the Core.
The situation remains fragile and I think the Jedi would rather risk war than lsoing 1,000 Jedi to the dark side.