Eh it's not really hard. You can either sit in its engines with an S/M where they cannot hit you with its turrets and keep on pelting them until enough crew leaves the ship so you can board it with a handful of marines.
I did it a few times and I now have 5 super-marines that can single handedly kill 30+ crew with ease xD.
As long as you don't DESTROY modules you can use L Miners/Traders in neutral sectors as practice targets for boarding to train your super-soldiers.
I do suggest that whenever you launch your marines you start circling around the ship you're capturing so they don't do something silly like shooting the landing pod of the marines.
If you aren't cruising in a 200m/s rinky dink vessel nothing except laser-turrets will hit you. And those don't deal damage so it's fine!