+1
Remember, one tool for the job. A tool can't do everything. The best is to have gofer to download/install/uninstall/update/remove individual packages inside the image, and metacello keep track of dependencies, configuration, groups of packages loaded together, groups of packages for distinct forks, etc.
And again, ScriptLoader, as I understand it, was never intended for public comsumption. It is in the image because the group releasing pharo and squeak was very small and needed a tool for preparing the image in a time when no proper package management tool existed. Now that tool exist and there is no reason to keep the old tools no matter how many pages you find in google pointing to obsolete instructions. They will be substituted by new docs/tutorials/blog posts that use the new tools.
Meanwhile, there will be confusion, granted, but in the end it will be better than the mess we have now.