It is a highly complex issue without an easy resolution, and not a whole lot of biblical guidance to get us to the point of understanding. However, I believe the threat to "kill" Moses is an allegorical occurrence, God not threatening the physical death of Moses' son. Such a threat violated God's premise of not visiting the father's sin upon the son. Therefore I refuse to believe God would make such a factual threat. But let's look at Moses' life to understand.
Moses had been raised in the house of Pharaoh, educated in the ways of Egypt, but still very much aware of his Hebrew heritage. So much so that, when walking through the fields, he defended a Hebrew man being beaten by an Egyptian, to the Egyptian's death. When, the next day, attempting to stop a fight between two Hebrew men, he realized his deed was known, he fled to Midian. And he fled not just to any house, but to the house of high priest of the people there, and eventually married the priest's daughter.
The religion of Midian was polytheistic. This was the influence under which Moses was raised. First among the Egyptian gods, then among the gods of the Midianites. Yet he still heard the call of Jehovah upon his life. Though he was symbolically with the house of the Midianites, culturally steeped in the ways of the Egyptians, he nonetheless was, at heart, a Hebrew.
Still, he retains great loyalty to Jethro, his father-in-law and longtime priest. Moses has been, at best, a very reluctant prophet to this point, arguing at times vehemently with God about his desire and abilities as the leader of the Hebrews. Obviously, the connection to the old polytheistic religions, and the questions and doubts they muster in his mind, must be severed.
Convincing the Hebrews of Moses' loyalty to their cause, and his qualifications as God's prophet was going to be difficult regardless. His lingering doubts made it even more so. To be recognized as the leader of the coming Exodus, he would need to separate himself from the ungodly religions of his upbringing and of his adulthood. God's threat to "kill" Moses' son was allegorical, again in my opinion, and in actuality a threat to Moses' prophetic calling.
In Job 2:9, we see poetic language in which "kill" does not have to mean causing the end of life. It could refer to the termination of the prophetic status. It is used there in a way in which the shouted words of Job's wife "Curse God and die!" seem to convey this meaning.
Also, in the story of Balaam the angel with the unsheathed sword is much better understood as a threat of killing prophetic ability. At this moment, what God expressed to Moses by threatening to "kill" him is the demand that the prophet dedicate himself totally and irrevocably to the people he is about to lead.
Zipporah, his wife, who stands as the symbol for his link to Midian, is the one who can and does terminate whatever lingering connection Moses may still harbor. The allegoric threat leading to the physical circumcision, carried out by her, terminates her and her sons' symbolic status as a connecting link to Midian. When she performs the only ritual which at that time connects the descendants of Abraham, Isaac, and Jacob to their God she expunges whatever loyalty to his immediate past Moses may still have carried.
Such a seemingly abrupt embrace of total belonging called for additional ritual emphasis. The severed foreskin is held up to express loudly that there is no return; it is held against the legs of Moses which can no longer walk back. The culture and religion of Midian are now reduced to a memory, and Moses’ position as the leader of the new nation of Hebrews is confirmed.
All strictly my opinion. Just FYI.