Yes.
It would be completely paralyzing were the executive largely staffed with those that wanted to paralyze it. Usually that's not the case.
I don't think that'd be case unless the orders were completely outrageous, in which case, yes, we absolutely want them disobeyed until adjudication could happen.
It might well be the case that, today, the executive branch (which includes essentially the entirety of what most people consider “the federal government”) is largely staffed by those who want to paralyze it.
You can certainly say that these people are right to try to resist the changes Trump is trying to make. But, like it or not, Trump is the democratically elected President, and it’s quite a challenge to come up with a conceptual model of American government that prevents him from exercising his constitutional authority over the Executive branch.