Ok, I figured out how to make the ending of the movie, which was the only part I didn't like, much better.
O
B
L
I
G
A
T
O
R
Y
S
P
O
I
L
E
R
S
P
A
C
E
Ok, everything happens the same way, up until Wash gets the stake through him in mid-quip. It still happens, but he gets it through the stomach instead of the chest. He's pinned to the chair, losing blood and consciousness rapidly. Zoe, instead of being stoic, flips out, breaking the facade of super-badassness for the first time. Wash and Mal keep telling her to go, there's nothing she can do for him, but she won't listen, and in desperation the rapidly failing Wash pulls Mal's gun, puts it to Mal's head and says he will pull the trigger if they don't leave. Zoe sobers up slightly, enough for Mal to pull her out of the room. Wash tosses the gun to Mal, the door closes, and four more spikes hit it, letting us know there's no way Wash could be ok.
On to the fight. After Mal leaves, things start to go wrong very quickly. In the space of a few seconds, a grenade buries shrapnel in Inara, Zoe gets knifed, Kaylee gets riddled with darts, and the doctor is shot. Simon tries desperately to care for everyone, most of whom are unconscious at this point, and River pulls her "Let me take care of you" bit, grabbing the bag, tossing it to Simon and shutting the door.
Cut to the Mal and Operative scene.
Cut back to River, fighting the Reavers. It goes as well as it did, until one of them gets a lucky shot across her face.
Cut back to Mal. He gets stabbed by the Operative.
The door opens. There's no sign of River, and Simon is staring at an army of Reavers. There's a creaking noise which keeps getting louder and louder. The reavers turn to look behind them...and the Serenity crashes through the wall, River at the helm. The Reavers are mowed down and crushed flat. She kicks open the cockpit window, and pulls Wash out with her.
Back to Mal and his victory. When he returns, River is carrying Wash's unconscious body and Simon is trying to support everyone else. The alliance troops show up, and there's no chance anyone would have time to react if they decided to shoot. The Operative tells them to stand down, and the rest of the movie goes about the same (except for Wash being alive.) You can even have the nice ending scene of River helping Mal fly the ship, as Wash is in the medbay with Zoe.
I don't know, that seems like it conveys the same "Oh my god, everyone's gonna die" feeling without having a sudden and pointless death.