"Directories with file extensions" (bundles) are a common way on OS X to bundle stuff consisting of multiple files into a single package, such as kernel extensions, iWork files (before iWork 09), iMovie projects, applications, etc.
You usually can edit an application's
Info.plist file to remove the definition of the offending bundle it defined — e.g.
.theme for iMovie.
.service is defined for system Services (see e.g.
/System/Library/Services — access them from the application menu bar item, then select Services), you'd probably break stuff by removing this definition.
If you're feeling lucky:
/System/Library/CoreServices/CoreTypes.bundle/Contents/Info.plist for example using Xcode (after changing the file and directory permissions using
chmod in Terminal) and remove the offending entry in the CFBundleDocumentTypes array.
You need admin permissions to do this. I recommend having current backups. It's possible something breaks if this association isn't purely cosmetic.