The Uchiha clan would be dead. If he decided to not take the mission Danzo would have given another the same mission, probably a root agent. Itachi would be cautious and expect some foul play from Danzo before the Civil war was definite and intercept the Root Agent during the beginning of the Uchiha Massacre. That would have started off the civil war, where the Uchiha would have attacked Konoha ninja. The shinobi would be at a loss at what's going on, and the Uchiha would get the advantage right away.
But it wouldn't take too long for other Root agents to arrive on the scene and either explain the situation, or buy time for the Hokage/Elders to explain it to the mass of Konoha. And at the time Konoha had a good deal of high level shinobi. Such as kakashi, Gai, Asuma, Hiashi, Danzo, Shikaku, Hiruzen. It would be a bloody battle, but Konoha would win.
As for Obito, he wouldn't even bother to interfere. No point, his enemies were fighting amongst themselves. So by the end of the battle, the Uchiha clan would be gone (No Itachi or Sasuke left). Konoha would have lost not only a clan, but a significant number of shinobi and be in an even more weakened situation (The Kyuubi attack was only 6-7 years prior to this, it's hard to imagine they've completely repaired and made up for losses from that).