Bingowings said:
Anakin doesn't destroy the command ship he just destroys a ship single handed and deliberatly (not by accident).
Once Nute Gunray is captured he orders the ships away (to save his skin) and the Droids power down on his command not because one ship is destroyed (which seemed a stupid way to run a war in the first place).
What about the deleted scene from AotC where Ki adi mundi boards the blue screened droid ship & deactivates the droids? would this not work for the final battle, Obi & Qui gon go after Maul while the other jedi take out the droids, anakin bows up the ship in his blue fighter (I love that mock up BTW bingo) & padme arrests Gunray.
Surley there is a high res version of the deleted scene out there somewhere?