I think I had thought about doing something similar, but I decided against using it for all ships since it'd be to unpredictable (There's been plenty of times I've not wanted to fire at a hostile for one reason or another, but with PD weapons you've got no choice).
My thought was different though, it involved Planet-type weapons and ships in addition to PD weapons. Turns out (AI) planet-type ships can't move very well or be target by PD weapons, so that didn't work.
I was trying to make it so that ONLY PD weapons could take out fighters. I think the reason most PD weapons won't target larger vessels (pretty sure they'll still do damage) is that they will waste valuable targeting time on targets that won't make a difference.
I didn't think that NOVA had high-damage missiles that could get shot down frequently to turn the tide of battle (basically to warrant using PD), but in EVC one or two missiles or torpedoes being stopped would save you. If that turret wasn't shooting the missiles and was shooting the ship, it wouldn't stop the (substantially greater) damage you would be absorbing, and would be doing little damage to the enemy ship in return.