The part that makes it not so clear cut is that this is really a constitutional issue rather than a criminal one. It is not credible that the judge was trying to ensure the man could keep living in the US undocumented. She was defending her court. From a judge's POV, arresting a plantiff/defendant in the middle of a trial is a violation of their right to a trial and impedes local prosecutors' abilities to seek justice.
Ultimately this seems like Trump asserting that the federal executive branch has unfettered veto authority over local judicial branches. That doesn't sit well with me.