re: Has govt ever defied a president like this?

Unless you happen to have original jurisdiction by the SCOTUS which only happens in very rare circumstances.

The identification of the countries included in Trump's executive order started with a law to restrict the visa waiver program to require that citizens of waiver countries, such as Canada, France, England, etc., who would otherwise be able to enter the US without a visa (just a passport) had to apply for a visa and go through the visa process if they had visited these identified countries.

It wasn't an Obama creation. The law was the Visa Waiver Improvement and Terrorism Travel Prevention Act. It originated in the Republican House and was authored by Rep. Candice Miller (R-Mi). The Act was tacked onto Public Law 114-113, which was the Consolidated Appropriations Act of 2016. The Republicans tacked it on as an amendment to the appropriations bill. The Act is 888 pages long. When it made it to the President's desk his choice was to sign it or shut the federal government down until the amendment was removed. He signed the appropriations bill and Rep. Miller's Act became law.

Obama did not authorize the Act or identify the countries. It was a Republican bill from the get go. Now it is being misrepresented as an Obama thing because he was the president. Anyone who does actual research, and truthfully reports what they find, will find out that everything written here is 100% true.

Except the Obama administration went back and added some countries to the initial list.