I say you just kill him in the same way you used to kill him before everyone started taking Big Turreted Ships.
Besides that, there are more options. The number of ways you can stress someone has increased dramatically. Also, there are more Ion weapons. Special abilities like Vader crew or Ten Numb w/ Mangler Cannon are also useful.
I think it will only suck when you only play big turreted ships. Personally, I hope to see a lot less of them in tournaments soon.