This issue has been hit before at other points in MODx. The main solution appears to be to give the user the choice of whether to do this or not and to warn them that if they do use absolute paths they would need changing if they ever moved the site.
If you look at Administration > System Configuration > Miscellaneous Settings in the Manager, you’ll see
"Rewrite image paths?" I’m not absolutely sure what this actually does.
More importantly, if you have TinyMCE installed, then in the section Interface & editor settings you’ll see that has a setting for Path Options. There are three options, Document Relative, Root Relative and Full Path. The help text says:
This setting tells TinyMCE how to handle the paths for internal links. Note: Document relative links may not work right with friendly alias paths. Also, links might need to be changed if you move your site to a different domain or subdirectory if links are root relative or full path.
It would thus make sense to have the same option available to FCKEditor.
I believe that you should change your files so that there is a config option in the include file (that defaults to the previous relative method as it is safest). Then if Bravado integrates this into the FCKEditor plugin/core he can add the option there so that it matches TinyMCE.