I recently had a problem with my laptop where I couldn’t update Adobe Acrobat because something had corrupted the installation. Acrobat (and the rest of the CS apps) ran fine, but I couldn’t update because the updater would throw an error, something about “source for the installation could not be found.” After much Googling and trying several options, I realized I would have to manually uninstall the whole CS3 suite and reinstall. Ugh.
Yes, it is okay to remove Bonjour after installing Adobe CS3. Adobe even explains how to do this. It would be nice to be able to unselect it during the install without having to perform a complex series of steps. But still, at least the uninstall is painless.