Has any one done this? I could try, but the server has been down for several days. :(
this answer comes a little late but yes, FastQC can read bz2-compressed fastq files directly since 2011. With BWA, you need to uncompress them first, but it can be done in a stream:
bwa mem ref.fa '<bzip2 -dc read1.bz2' '<bzip2 -dc read2.bz2'
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