I had the same problem. The following blog post helped me resolve it: http://www.polak.ro/svn-e200030-sqlite-database-disk-image-is-malformed.html
You do an integrity check on the sqlite database that keeps track of the repository (/.svn/wc.db):
sqlite3 .svn/wc.db "pragma integrity_check"
That should report some errors.
Then you might be able to clean them up by doing:
sqlite3 .svn/wc.db "reindex nodes" sqlite3 .svn/wc.db "reindex pristine"
If there are still errors after that, you still got the option to check out a fresh copy of the repository to a temporary folder and copy the .svn folder from the fresh copy to the old one. Then the old copy should work again and you can delete the temporary folder.