Light or Dark magic.

Destroying one skill slot... I don't quite get it...

I understood it this way: I'm leveling up a Dark faction hero against a Necropolis hero for the sake of getting one specific perk.
Conclusion: in total (not counting the racial skill), you can take 5 skills, and you've already sacrificed one, leaving you with 4, meaning you've lost something more useful. That's what I meant by

Destroying one skill slot