On a commercial airliner or even a DoC airplane flown by a professional crew of two, no increased risk, no problem.
Well, since that's not what you originally said, it's rather hard to guess.
Why not simply require that it be a commercial operation, then? I'm not really seeing how it shouldn't have been one in the first place for this event, really.
But then again, one doesn't see too much argument for making Dog the Bounty Hunter hire a cab to transport people or stick them on a city bus, either.
Society gets to vote on how prisoners are transported on the ground, and seems "okay" with private carriage there.
Since society doesn't really vote on air carriage rules, it seems like if this flight was somehow legal (again I don't see how it could be with recent FAA events surrounding ride shares and holding out) then FAA hosed the prisoner-pax, and if it wasn't legal, the point is moot.
Well maybe not moot, but only an opinion of what FAA should do, or already did.
Maybe an example of rules not being followed also, perhaps.
What am I missing? I don't see how slapping a prisoner who's also your meal ticket in the back seat of anything, and flying from one point to another, could ever be interpreted as needing to be anything less than a Part 135 operation. Do you?