Heat water to a low boil. Add sugar and hibiscus flowers; stir until the sugar has dissolved. Remove from heat and allow to cool. Strain; discard hibiscus flowers. Add grapefruit juice and mint and mix well. Refrigerate until cold, about 4 hours.
Pour chilled mixture into an ice cream maker and churn according to manufacturer's instructions. Add pomegranate seeds 5 minutes before the granita reaches the soft-serve stage.