I have to say that I consider your suggestion awful. Torpedo cruisers are not only cruisers, they are just the wimpiest and weakest cruisers around when it comes to defenses, having hull, shield, and armour like a LRM frigate and dying easily to a minimum amount of focused fire from cruisers, cap ships, strikecraft, and even frigates. Increasing their cost to make them prohibitively expensive, as you suggest, would render them completely worthless in any and all circumstances save those where you are unopposed. There's no way a mere 2-3 Torpedo cruisers should be allowed to survive for more than 20-30s of combatr in any defended gravity well - if nothing else, they make excellent targets for strikecraft.
As for Torpedo cruisers shooting at other ships, while I would prefer it if they did not due to aesthetics (it looks wrong and the only reason they are doing it is to avoid the micromanagement of having it as an activatable ability), the damage they deal to non-structures is miniscule: 1%. They are supremely irrelevant in a fight between two fleets duking it out. It looks impressive but you'd deal much more damage by having a third their number in scout frigates - a base 3 laser damage from the scout is a very significant damage upgrade over 3 Ogrovs when fighting other ships.
Torpedo cruisers are moderately expensive, have low survivability, and have only one single role they are good at - and that only when brought in large numbers or when the enemy ignores them in favour of other targets.
The only really big issue I see with Torpedo cruisers right now is that the AI does not assign them a high enough priority for destruction allowing a human player to get far too much mileage out of them.
