I'm no expert (as I wrote), but afaik the app install process (iTunes style) is sidetracked by running a program to install an App on your trusted computer.

Then you run the app.

I only use iTunes when I update the music on the iPhone, not programs. I assume most people do the same these days. (iOS 5?)

(But certainly, there is a possibility here -- maybe iTunes might tell the iDevice to update an application without informing the user? I can't say, Objective C was too much like Java for me. :-) I don't keep music on the iPad, so that is no problem.)