There is a very simple solution to both of these problems.
Don't make a Tenebrium skill. It's not needed. It adds nothing to the game, and REMOVES quite a bit. Instead, simply give each character a talent : Tenebrium Training - no longer recieve Rot from Tenebrium.
You could add T to weapons, but it works exactly like every other method of enchanting.
When I add fire damage to my sword, I don't have to rely on 'Fire Skill', it just adds bonus fire damage. That's how Tenebrium should work.
I really like this idea.
Tenebrium Handler (talent)
Prerequisite: Level 15
You no longer contract Rot from handling Tenebrium.
Note: Received as reward for Brandon's quest (even if you don't meet level requirement).
Tenebrium Warrior (talent)
Prerequisites: Level 15
You deal 10% increased damage with Tenebrium weapons.
Note: Received as a result of using book found in Sacred Stone (even if not meeting level requirement). The book does not grant the Handler talent, which must be earned or taken separately. Using the book fails if the character already has Tenebrium Knight.