You can litigate disproportionate fines, and there's a general requirement for proportionality in both EU law and under the ECHR.
Again, people are assuming that this is the first and only directive that has fines associated with it. It isn't. You don't hear a lot of people talking about the three month prison sentences possible for CE marking, for example - because very few of them have been handed out and only for egregious violations such as unsafe machinery that has caused injury.