My limited number of contacts at MS tell me that an Enterprise deployment solution is coming, but they couldn't get it done in time for the initial release.
It's improved with IOS4 as you can now deploy wirelessly by having the users visit a web site. With 3 the only way to deploy was using the configuration utility or have the users install with iTunes.
What we keep begging them for is the ability to point out users at our own enterprise app store, hosted on either Apple's servers or our own. It's also what I keep telling MS whenever I get a chance.
It's impossible to distribute an iPhone or an itouch as the user interface to custom hardware. It's also impossible to distribute an internal application if you only have 499 employees.