I think we all knew from the start that the shortsighted Separatist Council was always pretty much doomed. You don't make "deals" with a Sith Lord. A Sith will use you for what you're worth and then eliminate you when you've outgrown your usefulness, as evident in EPISODE III when Anakin/Vader takes out the whole group in one big Mustafar massacre.
Making them think they were being protected, Darth Sidious (via General Grievous) moved them to Mustafar, where no one would think to look or want to look for that matter. There seems to be a slight contradiction as to when Grievous originally filled the council in on this move, when looking at some of the published materials. In the comic, Grievous tells them he's moving them right after he lands on Utapau near the beginning of the film - and this is before he talks to Sidious. Most other materials, however, have Sidious telling Grievous to do this when they're talking via hologram. Here's the version from the published script, and note the omitted battle droid dialogue which you can also see in the EPISODE III Comic Adaptation, albeit slightly different:
71 EXT. UTAPAU-LANDING PLATFORM-DAY
A small NEIMOIDIAN SHUTTLE lands. BATTLE DROIDS surround the ramp as GENERAL GRIEVOUS descends onto the platform. SUPER BATTLE DROID G21 approaches.
SUPER BATTLE DROID G21
The planet is secure, sir.
The population is under
Good. Where is the
SUPER BATTLE DROID G21GENERAL GRIEVOUS takes the elevator to an upper level. He enters a conference room and presses a series of buttons on the table, and bows.
This way, sir...
72 INT. UTAPAU-CONFERENCE ROOM-GRAND CHAMBER-DAY
A hologram of Darth Sidious appears.
Yes, Lord Sidious.
General Grievous, I
suggest you move the
Separatist leaders to
It will be done, My Lord.
The end of the war is near,
General, and I promise you,
victory is assured.
The hologram of Sidious talks to GRIEVOUS about the death of Count Dooku.
But the loss of Count Dooku?DARTH SlDIOUS
His death was a necessary loss,
which will ensure our victory.
Soon I will have a new apprentice...
one far younger and more
powerful than Lord Tyranus.
There are a few other lost lines of dialogue in there. Nothing all that complicated or important, just extra words, really. It's interesting to note that in the screenplay, Grievous asks where the Separatists are but in the finished film, they're standing right there when he comes out of his shuttle.
Flash-forward to near the end of the film when Anakin/Vader arrives on Mustafar to tie up a few loose ends. Vader's initial run through the room appeared to have been much more gruesome than what we saw in the film; heads rolling everywhere, lots of chaos. Here are two excerpts from the published screenplay:
178 INT. MUSTAFAR-MAIN CONTROL CENTER-DAY
ANAKIN ignites his lightsaber, NUTE and the OTHERS panic. The DROIDS at the controls and the GUARDS grab their weapons, but it is too late. They are cut down in a flash. The Separatists bang on the doors, and NUTE and RUNE HAAKO flee under a table.
ANAKIN, stone-faced, moves through the room like the grim reaper. Bodies drop everywhere. SCREAMS are cut short as the head of the Banking Clan dies.Then POGGLE THE LESSER loses his head; WAT TAMBOR, SHU MAI, and the REST OF THE SEPARATISTS run into the conference room.
182 INT. MUSTAFAR-MAIN CONTROL CENTER-CONFERENCE ROOM-DAY
After everyone in the Main Control Room is dead, ANAKIN moves to the small conference room where WAT TAMBOR. SHU MAI, and some OTHER SEPARATISTS are hiding. RUNE HAAKO tries to run but is trapped by a dead-end as ANAKIN advances.
RUNE HAAKORUNE is cut down. NUTE GUNRAY crawls out from under the table and opens the Main Door, allowing DESTROYER DROIDS to enter. WAT TAMBOR is cut down, along with SHU MAI. DESTROYER DROIDS appear in the doorway and blast away, causing total destruction. When the firing is over, ANAKIN is gone. Blown away? No. ANAKIN drops from the ceiling behind the TWO DROIDS and cuts them to pieces before they know what hit them.
Stop! Enough, this is
Poor Rune Haako; he always was a bit skeptical of this deal with the Sith and now he knows he was right. His line of dialogue never made it into the film, however. The scripted version seems to give mention to specific members of the council but in the quickly edited version in the film, we don't see much special attention given to them. There's some photo evidence, however, that Wat Tambor did have a special death, originally meant to be clearly seen on screen. You can see the photos below. Also take note of the slight differences in dialogue in the EPISODE III Comic Adaptation, which was largely based on early versions of the script.
The part where Sidious asks Gunray if he's shut down his droid armies never made it into the film and as you may have noticed, Anakin and Sidious have a similar conversation after the slaughterfest. You can catch a quick shot of Sidious and Nute being filmed in the Starwars.com web documentary series (#15 - The Creatures of EPISODE III). This is also available on the Revenge of the Sith DVD. They're saying the lines you see in the comic below about shutting down the droid armies.