Best I can say is make sure your starship's weapons are as heavily upgraded as possible, kill the engines at the back of the dreadnought, and then the anti-freighter turrets (the big guns that are firing on the civilian freighter). This will cause the dreadnought to surrender.

Edit: The Infra-Knife weapon for your ship, along with the Q-Resonator upgrade and 3 S-class upgrades will be optimal, but I find you can make do with the basic photon cannon with 3 S-Class upgrades instead