It seems to me that, especially with an upcoming steam release, the game should at least look to mitigate ways players can actively hinder newbies.

This just seems like an oversight, and likely the exception because I can't really imagine any other ways to influence another player's journey negatively beyond this sort of thing (maybe the cauldrons, but they're pretty ominous, I guess.) - Most items inform the player that there is a potential consequence on use, not for just picking it up.

Anyway, the obvious solution in this situation would be to simply make it so picking up yellow crystals requires X mining skill: "You require at least level 25 mining to pick that item up."

I'd guess as time goes on this sort of thing would become more common, so it makes sense to introduce a safeguard sooner rather than later.