My suggestion would be to keep the stacking mechanic and make it +4 per stack. You can proceed from there by adding more stacks or even applying conditions based on the number of stacks (E.g. 4 stacks causes inhibited or eviscerated 5 etc). Just throwing ideas out there.
Protective being capped at 3 basically reads 'sacrifice a 70+ nora champion for 6 damage for 1 turn...your opponent decides when and where this ability activates.' Sounds more like a -nora ability. Just remove the ability altogether and give +2 base damage to runes that had it...
Well I for one don't mind the cap, it normally only goes around 6 anyway, unless you have some crazy tank. And my champions really don't die that easily.
A cap is fine now that most of the damage stacking has been lowered. It is just in this case, 4 nora is expensive for an ability that does nearly nothing unless you are losing a champion. What if it was just a flat +3 damage? But if your opponent KILLS a champ it also gains multi-attack 2 for 2 turns? Honestly, I think the old version of berserk 3 would be fine since your opponent is deciding when/where you get it. This means they will almost have an advantageous position when you get the bonus, if you ever even get to benefit from it at all.