I don’t know the specifics off the top of my head, but it is possible to “flow” values that are secret through a checkpoint file. (So that the resource input/output would be a secret/encrypted in the checkpoint file.)
It might require changing the resource provider however, so that the resource inputs/outputs are marked appropriately to get that behavior. But it’s certainly possible, and from what it sounds, what we would want to happen in this case too.