At the same time part of me wonders if it was unintentional. With their lives being so long, it is like the blink of an eye to wait for him. So the standard operation could very well be to infiltrate at first to understand the culture and planet.... but it could have been unplanned that he took a wife and had a son. But he told himself that he was still serving the empire by creating another Viltrumite, and then he would wait to see if his son got powers and when he did the game would be on.
But then in the end he couldn't go through with killing his son because he had changed from his time on the planet and the unplanned family. So he's now got an inner battle between loyalty to his planet and to his son, so he just Fs off into space to think.
This is also why it is so shocking that he has abandoned his post, and why nothing like this has happened before... because he did go "off script" with having a family.