I think it's a choice the player can make and live with the consequences.
I choose to leave the helmet off, and I am glad there is a penalty. It gives meaning to the choice.
Although I agree fully on choice having consequences, they also have to make sense.
When not wearing a helmet causes a penalty in stamina, something is wrong somewhere.
Helmets should penalize stamina (but add armor) depending on how closed they are.
Masks could have better enchantability, but even higher stamina reduction and less armor value.
Those ringlets (?) somewhat less enchantability, but no armor bonus or stamina reduction.
The perks should then not kick in if you're wearing armor of different class or material.