Thats a good point. Even if the torpedo cruisers phase in at point blank range against a star base, they will tend to do tremendous damage before they can be taken down.
I just don't like the idea of the torpedo cruiser at all though. Why does something that can destroy structures in seconds not hurt regular ships at all. It makes no sense.
My idea for rebalancing them:
Give them more range, and slightly slower speed. These ships should get maybe 30-50% more weapons range. to help keep them out of the skirmish. It also helps them to start doing damage sooner.
Lower their base damage amount. It should take longer to bring down a starbase than it does now.
Remove the damage inhibitors against other ships. 1% is really strange. These are obviously powerful weapons and they should be able to hurt everything. or at least something more reasonable, like 50% reduction. or whatever playtesting finds appropriate with the next change
Add a minimum range. Like submarines, torpedoes have an arming time, it won't allow itself to detonate while its still too close to the ship that fired it. Increase the minimum range of torpedo ships to the average range of other frigates. They would be helpless to fight back against anything attacking them directly. This will leave them vulnerable to faster frigates that can chase them down without fear of being fired upon.
Make sure they are vulnerable to strike craft
edit: also make the torpedoes dumb fire, with only a very weak homing ability. Fast ships can evade them rather easily. This will only make static defenses worth shooting at.