Our balance of powers works that way, it's not a novel concept that was just invented. The president does not have some special power because he won the electoral college election, majority of voters, plurality or whatever. He still has to follow the rule of law, he still has to obey court orders. If the president does some action that a federal judge rules was illegal, then they can stop it. This is completely ordinary and every president faces this, Biden, Trump 1, Bush2, Reagan etc.