In order to give someone money belonging to the government, the person doing so must have the authority. This authority to spend derives from the budget passed. If the law states that the state is not entitled to that money, then someone handing out that money is either making a mistake - and refusal to return it is a crime - or the person handing it out is committing a crime. The president might pardon others, but they can also rest easy in the knowledge that unless they get a clear pardon before the impeachment happens, they too could go down with him.
If the president makes a point that he does not have to obey congress on a fundamental matter like only spending what is authorized, then sooner or later congress will tire of the game and impeach him. Playing by the rules is fundamental to organized government.
The congress can always impeach any judges that refuse to convict a clear violation of the law. The president himself will presumably end up in a “night of the long knives” firing anyone who refuses to break the rules along with him.
I can only imagine such a scenario when the dispute is so fundamental that the two sides cannot reconcile. Politics is the art of compromise, and one facet is to recognize that if the votes are against you, you’ve lost. You cannot ignore the process; if you do, the country descends into chaos, since in this situation half the country would support one way and half the other.
The last time this happened, it took Generals Grant and Sherman to straighten things out. The closest example today would be, maybe, the abortion debate. Yes this is straying into GD territory but consider - even the most radical anti-abortion types do not try to refuse to obey the law (except the people that blow things up). They may pass laws nibbling at the edge of what the Supreme Court says is legal, and then see if the next ruling allows taking back that much. But everyone plays by the rules as set - otherwise there may as well be no rules.