If we grant those legitimate reasons (none of which are quoted in the stated justifications for the EO given to date by the White House, but which are, if true, certainly reasonable grounds for executive action) - If the concern is with visas issued in a given time period, from particular offices, via particular channels, then direct CBP to stop people for additional screening or refusal to enter if they present a visa issued in that time period, from those particular offices, via particular channels. Every US visa has all those details printed on it. You get all the benefits you want - time to rescreen those visa holders whose visas may not have received adequate screening - without causing massive confusion and inconvenience to travelers whose visas don't need to be called into question.
Such action would be fully backed up by the precedent of what Obama did in suspending the Iraqi asylum application process for 6 months in reaction to specific risks that had been highlighted in that process.