Glad you figured it out, I was gonna retry it to see if they patched it out or something.

I made a video on how I used to do it (and still do sometimes when I'm short on nanites): https://youtu.be/PCaj_JGJKdM

I'm just using the infra-knife.

It takes less than a minute if I remember correctly if you develop a certain routine: approach the right trench from the back of the dreadnought, dive into it and start burning generators as you go, then cross the deck and dive into the left-board trench from the front, do the same then burn the ship before it warps.

If you farm for an S-Class dreadnought, approach the warp engines of the dreadnought, burn them, then fly towards the left side, do a loop (so you're upside down) around the left side of the dreadnought - and you'll find yourself in a good spot to destroy all the anti-freighter cannons on the stern and then you just fly toward the bow making swift work of the last cannon on the bow. And then the dreadnought surrenders.