It is a basic law of physics that a sudden incident involving a large mass moving at relatively high speed is going to be more destructive than one involving a small mass. So no real surprise that HGVs are involved in more serious outcomes. And 'yes', reducing lorry traffic will undoubtedly make the roads safer.
Nevertheless, a quick skim of RAIB reports will show a disturbing number of rail mishaps involving freight trains (or other movements operated by freight drivers and with similar characteristics). These include runaways due to poor train preparation or in freezing conditions, serious wagon maintenance defects, empty containers blowing off trains, staff affected by fatigue or distraction, unevenly loaded wagons and so on. This is quite apart from non-train issues like defective track, landslips, etc. The industry has been extremely 'fortunate' that some of these incidents haven't involved multiple fatalities. Using the principle in the first paragraph, an incident involving a 2,500-tonne train is potentially far more destructive than even a 44-tonne HGV.
Turning back to the environmental issues of the slate waste traffic in particular, it is regrettable that bulk material has to be transported so far to the cement works. This has only arisen because local supplies of suitable shale are nearly exhausted. The whole reason for works being in Derbyshire originally was the availability of most of the ingredients for cement manufacture close at hand, with a low transport cost and environmental footprint. To make matters worse the manufacture of cement liberates large amounts of CO2 from the limestone, quite apart from burning an interesting mixture of coal, tyre waste and RDF/'biomass' (don't ask...).
Ways of producing cement more efficiently in terms of emissions are being explored by various companies and may well lead to changes in the nature (and location) of manufacture over time. It is a lot more complicated than just "Yippee there are new freight trains on the North Wales Coast".
