That is there to add a little risk/reward to interacting and researching the crystal. There should be an option to save the person (they walk away with minor injuries). Basically, the more the crystal saves lives and the more power is drained from it, the “hungrier” it gets when dark which gives it that chance. If enough souls are fed to it to balance the cost, it might even go “light” again and be used without any danger. There may be a crystal ability or two that only are found and used on the darker side of the spectrum.
TLDR: If you want to use it without risk, learn the “Sacrifice” ability, grab some crappy random NPCs and feed them to it until it goes Light again, then watch for if it starts going “dark” when you use it. Any major events like saving lives with immortality is what drains power from it and darkens it.