As for the Self-Destruct Device, you could mod the game with an Ion Cannon component and set it to kill electronics.....
(Electronics being, say, Planet Destroyers with value 0 or something else, and the Ion Cannon would have a damage type Only Planet Destroyers.)
Otherwise, well, if - IF - he's neglected to put selfdestruct on his ships, use a fleet with about one quarter fast capture ships (Escorts for the unmodded game), perhaps some large DNs or so with Boarding Parties - i.e. retail and wholesale Marine ships
- and the rest should be a mix of a small number of regular warships, and a lot of ships with only Engine Destroyers as a weapon and another with only Weapons Destroyers. If they use shields, add some shield depleter laden ships for flavour. Move this group of ships to the enemy, the boarding ships keeping a little to well back. Deplete their shields, destroy their weapons and eliminate their engines. Then send in the Marines.