Your question unnecessarily posits a conflict between a supernatural presence and a substantial one. Jesus is both substantially present (bread and wine really become his body and blood) and supernaturally present (transubstantiation occurs by the supernatural action of God; the accidents of bread and wine remain without the substances of bread and wine).
In consuming the eucharistic elements, the physical mechanisms of eating injure only the accidents of bread and wine. The process of consuming the host doesn't involve ripping and tearing Christ's body, despite its substantial presence. This is why the charge of cannibalism won't work.
We can still say Christ's flesh and blood are consumed sacramentally in Holy Communion because what is eaten is literally his body and blood, even if the physical action of eating affects only the accidents of bread and wine.