Surely the Captain of an aircraft has the ultimate descision to override any law in his duties of maintaining the safety of his aircraft.
Pace, this was not a case of a safety concern overriding the law. We were not talking about a flock of birds in-flight on a collision course, but rather wildlife being disturbed on the ground by pilots overhead at 1450'.
Looking at the letter of this wildlife protection law, what the pilots should have done is not overfly this nature reserve at any height where this might disturbe wildlife. Not at 1450' (50' below the base of CAS) like they did, not at 2000'-FL45 (typical CAT vectoring altitudes for EHAM at this location) and not at FL100 or above. Unless they were absolutely sure that their appearance/shadow/exhaust gas/noise/karma could not, in any way, disturbe the wildlife there.
That's the main problem we're talking about. It's not an aviation law but a wildlife protection law resulting from European legislation. The way that wildlife protection law is currently written - and apparently interpreted - is that it has no vertical limit. If your plane, no matter at what altitude, is thought/observed to have disturbed wildlife in that area then you're a target for prosecution. Even if you fully comply with other laws, including those for aviation.
Of course the Natura-2000 wildlife reserves (note: plural - there are several dozens of these identified in the Netherlands alone) are not listed as such on any VFR or IFR aviation chart. Furthermore, pilots have no way of knowing how skittish the animals are at that time. Have they eaten recently? How many natural predators are there in that area anyway? How used are they to overflying air traffic, or, for instance, traffic noise from a nearby highway or railway line?
(Note that in this particular case, the Oostvaardersplassen, a railway line literally run along the fence of the nature reserve and the highway A6 is just 750 meters away. If a train passes and a bird within the reserve is disturbed and takes flight, theoretically the train driver can be prosecuted too.)
So abiding by this law is a totally hopeless proposition. Not just for a pilot overflying this reserve, but also for a train or car driver on the nearby railway line or highway.