Thank you @BenKaehler. Yes, I would be very willing to share some of our data. I will PM you my email.
I have searched widely throughout the available bioinformatics programs and have only come across...maybe one or two programs for incorporating BLAST output into a biom-compatible format (and if I am missing any obvious/new programs, please let me know). And those few programs don't have the powerful infrastructure to continue on with other analyses the way Qiime does. Maybe the novelty and the potential use for non-microbial researchers might add an extra incentive for a developer to create such a tool?
Thanks everyone for their input. I am open to any further suggestions.