What if the player using missiles and torps was allowed to adjust their load out between matches? Have a rule that makes assigning missiles bombs and torps part of the deployment step and not purely list construction. I think the side board should be limited to no more than double the points allocated to ordinance so the player still has to plan ahead a little. Placing the stuff as you place your ships also mitigates some of the advantage if the player doesn't have pilot skill.
Finally if you take more than you have points for your opponent gets to re select for you to keep things honest.