Nice Mod.
Thanks! Glad you enjoyed playing with it.
Though imho The Zolf Class is too powerful once you get lvl 3 Mobile Space Mine Burst.
It launches 5 mines every 2 seconds for only 4 antimatter per cast (which allows you to cast it dozens of times) which do each 1200 damage. You can easily kill entire grav wells with defenses and enemy fleets with just that one ship.
So it goes when recreating source material.

It's designed to have a sustained rate of fire of 1 mine/second, and to carry 76 mines.
That said, sieging a defended system is exactly what the Zolf II does best. It has long range, high power. Its disadvantages are its slow speed, limited combat endurance, and relatively low hit points. Your best bet for preventing a Zolf from annihilating your fortress system is to kill it before it gets there.

You can also park some destroyers at the edge of the gravwell. A dozen or so should be able to instantly kill a Zolf when it warps in. Even if you lose the destroyers, removing your opponent's Zolf is a priority. (The destroyers may be too expensive currently for this to be cost-effective. I'll look into possible making them cheaper.)
Even if the enemy has some flaks you can easily overwhelm him with mines and some micro management. It's fun against the AI to do that, but imho not really balanced.

How many flaks are we talking about? In my testing 10 or so flaks, properly positioned, will virtually negate a pair of Zolf II's. It does require a bit of micro, but since the Zolfs require micro to efficiently target their payloads, that seems fair to me.
One other factor is that point defense isn't as common as it's supposed to be. In the source material, every ship carries some amount of point defense. Escorts just carry more, with better range and power. Try to imagine things if a group of 4 Roil destroyers had the same flak power as a single escort does now. Unfortunately, until the Forge tools come out and I can put in new models, all of the Sins frigate models support only one weapon system.
I think the bottom line is that the Zolfs are working perfectly fine. The problem is that the counters for the Zolf are a bit underpowered, mostly for reasons beyond my control at this time.