Seeing as Gunray orders his droids to destroy what is left of the Jedi wouldn't it make more sense to kill them with something more destructive?

Poisoned gas would leave an entirely intact corpse, flaming gas would leave a smoldering room with a few remains for the droids to dispose of as ordered.

You could have the protocol droid hobble out with half of it's coverings melted off (using See Throughpio as an fx reference point).

The Jedi could have made the same escape that Obi-Wan and Anakin do in the deleted scene in ROTS (by cutting a hole in the floor).

You might even be able to fabricate a shot looking up at of the droids looking down through the hole.