The mainproblem regarding damage difference between weaponbased Warfare and Ranger skills and magic skills is: Finding a good highlevel weapon is sufficient to increase your damage largly. While the damage of mage skills depends mainly on your level. At the beginning also from your int, but the higher your level is, the worse the benefit from int gets. So a mage can hardly increase his damage just with finding good equipment.
^ this. Sundering cleaver, anyone?
But seriously, I don't think that increasing the ap cost for 2h skills will balance things out. The main problem seems to lie in good measure with skills; for example, everybody seems to agree that the uberpowered crippling strike could use a hit from the 'ole nerfhammer. But raising the AP costs? This means that 1 handers will be able to use uberpowered skills with more frequence.
Edit: perhaps there could be another way of balancing things out, and that is modding warfare in order to boost the shield parry chance with each point. Since the shield parry negates damage, that'd definitely improve the survivability of 1H + shield users. Of course, this would have to be coupled with some small nerfs to other departments.