As long as you have JTL you can shoot the turrets/board the ship. Just as long as your invited to fly on it by the pilot.
As an aside....The Operations officer can use the ships droid computer, aka the pilot's loaded programs in FC,(you can't use your own). If you decided to fight on a MP ship I suggest putting together a good crew. 1 Cpt.(pilot), 1 Ops Ofc., 2 gunners, 1 Med Ofc., 1 Engineering Ofc. this is 6 peeps to run a MP ship properly. More would be helpful with med training and fire blankets at the ready. Make sure that the Eng Ofc. has conduit kits, generic repair kits, etc etc. So he can fix plasma leaks and make repairs. The minimum on a MP fighting ship is 2...I wouldn't chance fighting alone on an MP without atleast 6 peeps who know what they are doing.