You can remove the RNA from the beads using proteinase K digestion, and follow up with your RNA isolation protocol of choice. You should perform a few washes of the beads using SSC or TENT buffer before the proteinase K digestion to reduce non-specific RNA binding.

Thanks for the suggestion Emanuel! Will give this protocol a shot as well.

I've also used Trizol/Qiazol directly on the beads with fine results.