The international legal position on this matter is clear. The US must permit entry and afford refuge to anyone it has recognised as a refugee or to whom it has granted asylum. Moreover, it cannot return any person to a country where she or he may suffer torture or other persecution. No ifs, no buts, no qualifications on national security.
Merkel will have reminded Trump that the United States is a party to the 1967 Protocol Relating to the Status of Refugees. This prescribed the continuing application of the 1951 Convention relating to the status of refugees which was adopted to address the aftermath of World War II. That original convention was agreed in Geneva so it is sometimes referred to as the Geneva Convention.
As the US voluntarily accepted the 1967 protocol to the refugee convention, it is legally obliged to implement it. Despite Trump’s personal complaints about these “rules”, all other states party to the protocol and convention can legitimately expect the US to comply – hence the expressions of dismay from other heads of state as Trump announced his executive order.