Unless you think you're smarter than US generals, I don't think they widely publicize that an attack on Fallujah is coming without expecting at least some of the enemy to flee. By the way, the chances of finding Zarqawi are higher in a city where he's not completely surrounded by his supporters, as the only chance would be to get a tip about his whereabouts (as happened with Saddam). You'd never get that in insurgent-held Fallujah. Why Allawi made that ultimatum, I can't speak to, probably mainly to warn the citizens of Fallujah that the coalition was serious about going in.
But again, this is a war, not a criminal investigation. The deaths of what will probably end up being close to 1,000 of the terrorist forces and the re-capture of their national base of operations is a greater victory for the coalition than capturing one man, however influential he may have been.
The process will probably get repeated in other cities serving as insurgent bases. It's a process that will probably take a long time but will gradually render the terrorists more scattered, less coordinated, and less numerous. Whether that's enough to go forth with some acceptable level of stability, we will have to see.