[Toadling]

I've seen this same issue. I believe it has to do with Spotlight still using the old OmniFocus' MetadataImporter (which allows OmniFocus actions to be search with Spotlight). I'm not sure if there's much Omni Group can do to work around this as I think the issue is actually with the OS rahter than OmniFocus. I've seen this with other apps as well; happens a lot when I replace an app frequently in beta testing.

Either way, if you wait a bit (as much as 30 minutes on my machine), the file is eventually released and you can delete it normally by just emptying the trash.

I've also noticed that if you do "Secure Empty Trash" from the Finder, it'll also deletes the file immediately, even if it's in use by Spotlight.

-Dennis