[curt.clifton]

Just guessing here, but are you trying to empty the trash immediately after upgrading? If so, what happens if you wait awhile before emptying the trash?

The OmniFocusMetadataImporter is an OF "plug in" for Spotlight that runs in the background independently of whether OF is launched. If Spotlight is indexing when you upgrade, then the importer can't be deleted until Spotlight is done with it. This would be true regardless of the automatic update framework used. That is, switching to Sparkle wouldn't fix this particular problem.