"yet immigration laws have been selecting certain religious groups and treating them more favourably for years now. The Lautenberg Amendment,of 1989, gave religious groups in the USSR including Jews, some Christians, etc., presumptive refugee status unavailable to non-believers or state-sanctioned religious groups that weren't persecuted."
The important word there is prosecuted. Countries recognize groups that are prosecuted in their own countries because of their religion, race etc and offer them safe haven as refugees.
That is not the same thing as discriminating against people on the base of their religion.
You are digging your own proverbial hole by mentioning this refugee status issue, which illustrates that US knows discriminating against a religious group is a bad thing, since it accepts refugees on the basis of it.
"So we see here when the principle of singling out certain religious groups was first established"
... to protect them against discrimination such as proposed by Trump in their own countries.
It is baffling that you can't see this.