My reading of:

http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

seems to suggest we want the current behavior. For example, one of their examples is the insertion GCG -> GCGCG. As far as I can tell, the variant allele length should never be 0: it should be the base before the deletion (unless the delation happens on the first base, in which case it is the base after the deletion).

We will need to revisit this when we support structural variants. I'm having some parsing issues on the VCF files I've tried with SVs, however. I will look into it. I think for now simplest is to make that a separate issue.