You cannot get rid of this problem. if you copied a directory/file, you have to include both(source and destination) into svndumpfilter.
However you can do some tricks:
if you dump a repoositry not from revision 0, but say eg. from rev.100, you will get a new repository with revision 1-100 vanished, however your destination repository has all files/folders in rev. 1 as your source repo in revision 100. In this way you can get rid of versioned data without loosing the HEAD-Revision.
You can try to dump/load your source repo until your first copy into a "flat" repo, then add the remaining dumps onto it. In this way you can skip the troublesome copy-from Revision, as your files are already in the fitting (destination) directory.