1.  Trump was planning this ban before he had any of that secret information; there's no actual rational basis for it, it's just his attempt to legally put in place the Muslim ban he spent the campaign advocating for.  Actual counter-terrorism professionals find this to be insanely counterproductive, as it harms America's image at a time when they need cooperation from people in the Arab world.

2-3.  It's a violation of the Establishment Clause, as well as congressional statutes relating to immigration, to discriminate based on religion, which is what Trump is doing.