"I had to shoot first," Chauprade said after Monday's surprise announcement that he was leaving the FN.
Earlier, he had explained his resignation was motivated by "moral" and "basically ideological" reasons.
The FN "pushed aside the man to whom we owe everything because he was no longer useful", Chauprade said, adding that someone capable of "betraying" he father was also likely to betray the French people.
The MEP was the leader of the FN's group in the European parliament but was replaced by Edouard Ferrand, after public statements judged embarrassing by Marine Le Pen.
Among them were remarks questioning the truth of the "official version" of the 9/11 attacks on New York and Washington, a video claiming that a Muslim "fifth column" constitutes a "serious danger" for France's future and, inside the party, claims that a "gay lobby" had gained undue influence, an apparent reference to FN vice-president Florian Philippot.
On Monday he also criticised the Philippot-inspired change in economic line as "outdated, socialist and statist", preferring a free-market position.
But it was the role of one of his assistants, Pierre Malinowski, in the flight of pilots Pascal Fauret and Bruno Odos from the Dominican Republic that appears to have brought matters to a head.
The two were sentenced to 20 years in jail for alleged cocaine smuggling after already spending 15 months in prison awaiting trial.
Malinowski, a former member of the French military, openly admits helping them escape and Chauprade supported him, claiming that the two were innocent.
Although the two will not be extradited, an investigation has been opened in France into their flight that could lead to legal action against Malinowski and Chauprade.
Le Pan tweeted that the affair meant that "our differences ... had become too great and his remaining in the FN impossible".
Ferrand has invited him to resign his MEP's seat.