That's actually fairly easy. Just attach this to your engine:
Ability 1 Type := Weapon Delivery Type Damage Received Modifier Percent
Ability 1 Description := Reduces damage from (weapon type) by 90%
Ability 1 Scope := Space Object
Ability 1 Range Formula := 0
Ability 1 Amount 1 Formula := -90
Ability 1 Amount 2 Formula := "Energy Beam"
and change "Energy Beam" to the delivery type of your new weapon. You may need to make a new delivery type to prevent it from affecting other weapons, and I'm not sure if this affects shields/armor or just internals.
EDIT: fixed sign typo.
