Sharing 0.9.7 code among multiple sites

My goal is to install the MODx core once and share it among several sites (one copy of the core directory with links from the web roots of the other sites, much like Typo3 does it). I hope that this will make maintenance easier. My first question is with the setup directory. I don’t want to delete the directory but I don’t like seeing the warning in the manager screen. I’m not worried about the setup directory being there because for the sites that I’ve already setup, I can modify the .htacess file to make that directory off-limits. I was thinking that I could modify the core to suppress the warning, but then I’d have to worry about making that update when I refresh from the SVN tree. Basically, I’m lazy, so instead I just renamed the directory. I’ll change it back to setup when I’m installing another site. Sorry that this is starting to ramble. The question is, is there a better approach for dealing with the setup directory for a multi-site install?

Thanks,
Mike