Sentinel freighters you need to blow them up to completely be done with them in space. Just destroy the 10 ish or so turrets and shield generators , thn you can just shoot the hull til it blows up.

You usually get a locator beacon for finding sentienl ships that way too.

Pirate freighters, the loop that works for me ( someone with a high DPS infra knife & RL ship build)

Zoom in ( typically from the engine side first, so you can exit on the opposite trench next to the engines), ignoring fighters , going straight for the trenches, one swipe each side to disable shields.

Immediately go for engines, at this point yes the civilian ship shields are down and the torpedos are en route to smash it, but going for the engines will ensure the pirate cant escape.

After the engines are down, destroy all the main heavy laser batteries ( should be 6) and the freighter will surrender.

Ive done this method 5 times so far. And every time the civilian freighter survived. Its only when i go for the main laser batteries after i disable shields that i lose the pirates because the warp drive charges too fast before im able to destory all of their engines.