Maybe you just failed to notice that Bonjour, QuickTime, and MobileMe are all tied to iTunes for functionality.
MobileMe is tied in to iTunes for iPhones, Bonjour is for iTunes Sharing, and QuickTime is required for iTunes functionality.
Safari has been known (recently) to prompt for optional installation, but is not checked for installation by default. Your wife would have to check the box and click the install button to "accidentally" install Safari. Also, she is prompted to install these items because the Apple Software Updater process is running on startup. Whoever installed iTunes failed to read and uncheck the box for it to not be installed.