Hey, this annoyed me so much I’ve added code to remove links in excerpts (and a setting if you want to leave them alone). Currently this is only in the TC:
NB: Update the TC first, then the theme sidecar plugin (you need both for this to work).
The result is now much cleaner and you can rebuild posts with oneboxes all you like and the links will not appear in the preview excerpt 
(NB Theme sidecar plugin setting!)
