Well, the big ship and huge flags won't have any effect on the damage, only on what it targets. beams are immune to some of the rules governing destroying things with the 'big ship' flag. puncture might help, but i'm curious about how much damage is 'too much'
I've built a slash beam that takes out subsytems and turrets very quickly, especially on cruisers and corvettes, It does hull damage too, but not enough that it will destroy the ship before its disabled. I went for a balance that would render the ship mostly disabled about the same time it hit 40% hull or so. The problem is that you have to actually do decent hull damage in order to damage the turrets, so turning the armor damage way down and the subsytem damage way up just means that you're going to take out subsystems, but not turrets.
One thing you might do is turn up the damage value and lower the beam duration. This makes sure that when a turret does get caught by the beam, it'll get a bigger chunk of damage without actually altering the total damage done to the ship.