How to read structural variant VCF?
I just received a reply from 1000Genomes regarding this. I'll post it in its entirety below:


  Looking at the example you mention, I find it difficult to come up with an
  interpretation of the information whereby the stated end seems to be correct,
  so believe that this may indeed be an error.
  
  Since the v4.0 was created, however, new versions of VCF have been introduced,
  improving and correcting the specification. The current version is v4.3
  (http://samtools.github.io/hts-specs/). I believe the first record shown on
  page 11 provides an accurate example of this type of deletion.
  
  I will update the web page to include this information.


So we can take this as official confirmation that we were all correct in suspecting the example was just wrong.