I don’t  see a Greek origin to House Harkonnen and I have a suggestion. If you base it on the works of  Aeschylus, the opposing houses can be seen as the King and Queen of Argos.  Clytemnestra, the queen, came from Sparta and descends from Zeus by way of Leda.

We know he House Atreides comes from  the House of Atreus (the King of Argos). The prince, Orestes, served Apollo when he killed his mother, who killed his father–the king. The god line of Harkonnen would be Zeus and at Sparta–sits the throne.

Spartan kings claim descent from Hercules and are called the Heracleidae. Harkonnen has some linguistic similarity to the Heracleidae, so my suggestion is the House Heracleidae.

I wanted to solve this for my own purpose. My novel will have an allusion to another daughter of Leda– Helen of Troy. After figuring this info out I have decided to make a niece; with an allusion to Orestes. I just have to figure out where to install it in my novel. Brian Herbert or other writers devoted to the Dune universe may find use for my suggestion.