We should ideally have some sort of slow, automated system - such as a shipyard that repairs block by block or something.
Replacing lots of small turrets is a pain in the ass - and, when I'm making someone I hate do it, an absolute joy for me. I'd be okay with automated repairs being considerably slower than just salvaging and respawning your ship, or manually building new turrets and patching holes by hand, as long as it can be done automatically while the chunk is loaded.
I strongly feel there should be both rewards for victory and punishments for not just failing, but failing spectacularly - it drives players to do better and gives everyone else the satisfaction of knowing the other guy will have to wait a good twenty minutes for his forty 5.0 mass PD turrets to be reattached, regardless of what kind of system it uses (hand repair via spawning BPs, or shipyard repair).