The Plague (Subverters, Boarders, and IDs, Oh My)

[inigma]

Oh, so The Plague would need their repair ships. Well, ok, that was already planned for. After all, with their primary strategy to board engine destroyed, mentally flailed sitting ducks, the other half of the fleet should consist of repair ships (albeit carrying additional subvertors or boarders).

[Suicide Junkie]

If you want to make a mod, you could also give the boarding parties the regeneration ability from organic armor.
You will need at least one surviving component with the ability to regenerate them, but you'd be able to make boarding attempts every few turns in combat as the parties get rebuilt.