I think this rule has a fair chance to survive:
1) Trump hates illegal immigrants. But Startup Visa (or any kind of Visa) implies only legal immigration path.
2) Trump doesn't like that immigrants take away jobs from locals. But startups tend to create new jobs, reducing unemployment.
3) Peter Thiel (Trump's new tech advisor) is a famous investor and a partner at Y Combinator. This guy needs new startups. Most likely, he will lobby Startup Visa initiative.