Federation Commander

Circumstances vary, and under different circumstances, the circumstances are different.

A Klingon penal ship that surrendered might be treated in any number of ways. If the ship surrendered legitimately (under conditions when any non-penal Klingon ship would have) then they'd be treated as ordinary prisoners.

A Klingon penal ship crew that surrendered for less than honorable reasons might negotiate to stay in the Federation for a long period of time.

In pieces?? We couldn't fit her with hellbores and gatlings and use her ourselves if she was in pieces

With the Kzinti, it's more likely to be the crew who are in pieces, lightly grilled in barbeque sauce...