I'm a Vasari player, but I'll try to give a hand...
The subverter's distortion field is powerful, but very expensive in terms of anitimatter. Some theoretical counters I can think of are:
1) Mass rush: (carefully spaced, perhaps subdivided into different fleets, so that when you see the subverters coming you can split your forces up)
2) Light frigate anti-ability abilities: Your Cobalts are pretty easy to spam, and you could temporarily cripple the subverters, long enough perhaps to take them out.
3) Out-Range: Shoot them from farther than they can jump. Your LRF's should do the trick. They also could have splash damage, so you could possibly roast several at once.
4) Decoy: send in a small force to coax the Subverters into crippling it, then send in your heavy cruisers (hopeflly they were sitting a safe distance away) to shred the subverters.
As I said before, these tactics are theoretical, and I have never tested them before. If any work, please let me know!

Best of luck!
ChaoticMagician

Thanks for the replies, guys

ChaoticMagician, your suggestion of providing a few 'sacrificial lambs' seems to work reasonably well. I tried with the very cheap cobalts, but frankly they just die too easily to be of any use against a large massed fleet. So, what I've been doing is just using my kodiac heavy cruisers in this fashion instead:

Select 5 - 10 'sacrificial lambs' depending on enemy fleet size. Send them in to the centre of the enemy fleet, ahead of the rest, spread out. This usually nets about 1/3 to 1/2 of the enemy subverters, and also helps draw the fire of the rest of the fleet. With the rest of my kodiacs, I split them into two groups, roughly 2:1 ratio. The larger group dives in and attacks any visible subverters, particularly those that look like they're lining up to jump in. The smaller group stays out of range until the larger group gets 'infected' with active subverters, then close in to take them out. When the number of subverters has been reduced to less than 10 or so, I start focussing on the rest of the fleet and using my cap ships to take out any remaining trouble-makers


The annoying thing about the subverters, from my point of view, is they interfere with my favoured method of attack What I like to do, when facing superior forces, is dive in with 80 or so heavy cruisers and a few cap ships, and cut down the number of enemy carrier craft to a 'managable' number - ie less than 30 or 40, then jump out. During this time I can often mostly replenish my losses, and next time I jump in I will have air superiority, so I take only half the damage-per-minute that I did in the first attack. On the second jump I target the main damage-providers - heavy cruiser equivalents and long range frigates. The third jump I like to just annhiliate the rest of the enemy fleet Having a superior economy allows this tactic to work well, as I can always replenish my losses faster than any *single* given enemy (if not the mass of enemies as a whole).

Oh yeah - glad to see that the subverter has been somewhat nerfed in 1.1!