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The context seems to be firstborn sons. I believe it was Moses' firstborn son he was going to kill as Moses had not circumcised him according to the commandment given to Abraham.
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The issue was circumcision, not Gershom's status as first-born. An echo of the story is seen in Joshua 5:
... all the people that were born on the way in the wilderness after they had come out of Egypt had not been circumcised. 6 For the people of Israel walked forty years in the wilderness, till all the nation, the men of war that came forth out of Egypt, perished, because they did not hearken to the voice of the Lord.. It was their children, whom he raised up in their stead, that Joshua circumcised; for they were uncircumcised, because they had not been circumcised on the way.
Moses' son was in the same situation as those who had been born during the Exodus. He needed to be circumcised because this ritual was the sign of God's covenant:
God said to Abraham, “As for you, you shall keep my covenant, you and your descendants after you throughout their generations. This is my covenant, which you shall keep, between me and you and your descendants after you: Every male among you shall be circumcised (Gem 17:9-10)
The text does not say that God "wanted" to kill Moses. The author of this passage, whether one thinks of him as Moses, God himself, or a later human writer such as a Levitical priest, wanted to emphasize that the covenant of circumcision was a matter of life and death.