If you rename the configuration folder you will need to uninstall any of the remaining extensions in order to get a proper installation of the extensions. If you leave any of the extensions there the configuration folder will become corrupted in the same way.
Are you still having troubles with this or is the issue resolved? Also when you mention that you had to remove a line of code to get SiteAssist to work please expand on this.
When it comes to these solutions to get past corruption and other issues these techniques come directly from Adobe, that is where we get them from. Here is a link to the kb article that talks about the issues in more detail.