Are these computer-controlled or your own piloted fighters? If the latter, you probably still at least have fore and aft thrusters. I don't think SS disables pitch, yaw, or roll thrusters, but translation thrusters can definitely be knocked out. If you therefore have the main engine intact, you should be able to nurse your bird back to the boat. (Note that I am coming from the angle of playing SS with "full realism," which is in truth actually semi-Newtonian.) IF THE FORMER, you may just be SOL. That would be a task for a mod/coding project; unfortunately, SS has not received the love it really needs in that regard.
...If you look at some of the other threads, you will see that there have been coding efforts in the past, but organization was never fully intact.