Watching some of Pagz TPM clips gave me a few ideas but I'm not sure if they are suitable for his project so I'm putting them here.

Going with the conventional start up wouldn't it make more sense if the Feds didn't show their battledroids to to Republican Ambassadors?

The ship could seem to be run by normal droids R2 Units etc but the mystery would be why hasn't any living being come to meet them.

The Feds note lightsabers on the CCTV (or whatever it's called in EU land ) which confirms their most feared suspicion that the Chancellor would send Jedi (delete droid line as it's no longer needed).

Gunray orders all his non-droid crew to stay away from them because they can read and twist their minds.

They then destroy the Republic ship just in case there are more Jedi inside.

The Feds could then torch the interior of the conference chamber (starting with smoke and then with flames).

Cut the shots of the droids waiting outside the door (or change the droid line to confirm there is nothing left of them), the Jedi have escaped up a ventilation shaft leaving a gutted room and a destroyed protocol droid.

The Feds then have their conversation with the Queen convinced the Jedi are dead.

The Jedi then try to get to the bridge and encounter the battle droids for the first time in two waves (first the normal ones and then the Destroyers) and get confirmation of the Feds intension to invade when they get to the hanger.