Or you appeal to a higher court.

Law is not static. Congress or Parliament makes its legislation, ambiguity arises in corner cases, Courts are asked to sort it out. Courts try to divine the intention of Congress or Parliament. If Congress or Parliament disagree with that interpretation then yes: it's up to them to change the law. Otherwise, by failure to further Act, they conceptually support the Court's interpretation of their intent.

To be fair, the original wording was pretty bad. If a non-profit had someone pay $1 into a political fund (potentially without approval) they could lose their nonprofit status.

This is obviously not the intent of the law, but would be the 0% everyone throws around.

You could say <1% or something, but now you are arbitrarily drawing a line. Thus I would point out that not drawing a line is by extension impossible.