This is unchartered territory. The framers of the constitution anticipated nastiness among the three branches, or else the system of checks and balances would be a system of "cordial deferments" instead.
That said, the executive branch has the moral impetus to ensure protection of citizenry under the constitution. Otherwise, there would be no reason for an executive branch. We could be ruled by legislatures and judiciaries who can hold unending pissing matches with no army to be led by either.
Great summation. If we allow the judiciary to rule, what's the executive branch for? We need this hit of moral integrity.