It might have been a little shady and corrupt, but it was basically a plea deal. He had letters showing the emperors intended return and revolution - which is treason. Notier wasn’t some underworld/unknown figure, he was a well known Parisian Bonapartist. And the Morrells were already under suspicion.

Danglars was an opportunist looking to make a political play, Ferdinand was a jealous asshole, but the worst thing Villefort can be accused of is being a politician. He distanced himself from his dad, he married into the bourbons. He didn’t exactly get along with the old man, but Nortier protected him during Bonaparte’s short restoration.

Young Eddie was a fool 10 different ways - Notier/Villefort notwithstanding. Napoleon had just been deposed and exiled. Marseilles was heavily royalist and anti-Bonaparte. Yet he thought nothing of just stopping by at Elba. And he wasnt naive and indifferent - he knew who he was talking to and he was proud to do it - though he kept the secret according to his captains wishes. He was first mate on a “smuggling” boat. How could he not know, hell the accountant (Danglars) knew. One look at the chart and it would be obvious they’re stopping by Elba to pass messages. He might have spent a couple years on boats, but daddy Dantes lived in town, Morrell lived in town. He had to know about the unrest - especially since boats carried word abroad to trading partners.

I don’t think Villefort had any intent of releasing Eddie at any point. Regardless of Bonaparte retaking the throne. A) he was a royalist, B) he knew it wasn’t going to last. Letting Eddie out after 3 months would out him as a Bonapartist like his father and kill his future in France. He’d be sidelined once Napoleon fell apart again. But he didn’t go so far as cutting Eddie’s head off without a trial.