First, I suggest you update your post to include a bit more information about your configuration. Are you using virtual servers within a single apache instance for the multiple domains? Are there multiple servers? Is all the "sharing" done via your automated CVS updating?

Assuming you have separate installations and instances, I would think that the most sane approach would be to refactor your configuration management code to handle multiple configuration instances within the SiteConfig.pm package based on some key provided at load time. So you would have distinct configurations for each domain all stored (or at least referenced) in the SiteConfig. Then load the appropriate one into the global structure at run-time.