I think you have to make a difference between Cadoudal, who had been an active Chouan leader, was undoubtedly in Paris on an anti-government mission and secured his fate by killing a police agent during his arrest. He got a public (if highly rigged) trial.
D'Enghien was not actively engaged in any anti-government activity, he wasn't even in France, and just being willing to do so does not make a criminal offence. He was kidnapped, taken secretly before a military court and given no chance to prepare a defence before being condemned and summarily executed. That stinks by any standard.