The problem is that we have two laws in conflict: the original laws forming the EPA (among others) from the late 60's to early 70's, and then executive orders which seek to mitigate them. . . [S]he is supporting the original (Democrat, I think) version of the law, and ignoring the (Republican) executive order that applies.

The problem with this reasoning is that executive orders are not laws. Remember separation of powers. The legislature makes the law, the executive applies the law, and the courts interpret the law. The President has no ability to make law. Executive orders are basically binding policy statements issued to federal agencies. A judge doesn't owe an executive order deference if it conflicts with the statute.