Build more than your opponent...I'm dead serious, build more than your opponent...expand faster, get more resources, build more corvettes...
After the initial rushing, integrating large amounts of flak is important, but in small numbers flak is just useless...
A discordia with fracture or a corsev with dem team are good AoE's to use against them, but the problem is that a capital ship just dies so fast against these things...
I know it sounds like a lame response, but really simply out doing your opponent in the empire-building macro and having more of these things is how you counter them at this point...