Asepsis prevents creation of .DS_Store files. It redirects their creation into a special folder.
At core Asepsis provides a dynamic library DesktopServicesPrivWrapper which gets loaded into every process linking against DesktopServicesPriv.framework. It interposes some libc calls used by DesktopServicesPriv to access .DS_Store files. Interposed functions detect paths talking about .DS_Store files and redirect them into a special prefix folder. This seems to be transparent to DesktopServicesPriv.
Additionally Asepsis implements a system-wide daemon asepsisd whose purpose is to monitor system-wide folder renames (or deletes) and mirror those operations in the prefix folder. This is probably the best we can do. This way you don't lose your settings after renaming folders because rename is also executed on folder structure in the prefix directory.
