How can I run iTunes without installing Bonjour in Windows 7?
not sure if this is what you are looking for but I have, on occasion, done a standard iTunes install and then gone into Programs and Features and uninstall Bonjour. That and Apple Software Update show up as separate items for installation.

What it then leaves behind, I am unsure of. You used to be able to run regmon and watch installs to see what it installed so you could then rip it out by the roots later. But I gather that it is no longer supported. Not sure if Process Monitor will do the same thing.