Quote 1
Villefort gave a bitter smile and said, in response more to his own thoughts than to Mme Danglars' words: "So it is true that every one of our actions leaves some trace on our past, either dark or bright. So it is true that every step we take is more like a reptile's progress across the sand, leaving a track behind it. And often, alas, the track is the mark of our tears!" (67.9)
Though he talks of all actions leaving a trace, it's the darker ones, the ones that stand out, like infractions written out on your permanent record.
Quote 2
"If he is arrested […] listen, I hear the prisons are overflowing—well, leave him in prison."
The crown prosecutor shook his head.
"At least until my daughter is married," the baroness added.
"Impossible, Madame. The law has its procedures."
"Even for me?" the baroness asked, half joking, half serious.
"For everyone," Villefort replied. "And for me as for everyone else." (99.80-85)
Though he may be corrupt, Villefort upholds the basic tenets of the law. He is impartial – at least in this case.
Quote 3
Villefort drew his chair up close to that of Mme Danglars and, resting both hands on his desk and adopting a more subdued tone than usual, he said: "there are crimes that go unpunished because the criminals are not known and one is afraid of striking an innocent head instead of a guilty one; but when these criminals are discovered—" here Villefort reached out his hand towards a crucifix hanging opposite his desk and repeated "—when these criminals are discovered, by the living God, Madame, whoever they are, they shall die! Now, after the oath I have just sworn, and which I shall keep, do you dare, Madame, to ask my pardon for that wretch?" (99.94)
Villefort does advocate what you might call extrajudicial justice, out-of-court justice, in certain cases. Some decisions regarding innocence and guilt are not meant to be made at the assizes. You can put this one in the same category as a duel.