First, i apology for my english but i will try to improve with time ...
Here are some of my toughts about the controversial story and ending of killzone 3 (really a masterpiece)
First some basic considerations:
1) Guerilla knows that out there most of the Killzone fans cheer for the Helghast side, so they would never wipe them out from the planet, they just want you to think so...
2) Killzone 3 has shown us that Helghast are, after all, like normal humans, greedy, power hungry, cruel and also corrupted (like the guards on the space station and Stahl private Army)
3) Irradiated Petrusite is not dangerous unless its charged someway, we can see it clearly in the first level, when Rico touch it and also in the mulyplayer level, one of them take place in an urban irradiated area.
4) Stahl is clearly alive, he escaped in a Leech pod and his troops recovered him, but since his plan have been ruined (for now) he will be pissed off... and cant wait to take his revenge on ISA and UCA. We can also hear him from propaganda messages in multiplayer, he says something like ... we work toghether, we are strong, this planet made us strong, we must thank our leaders for betraying us...
So lets begin:
Our little Stahl escaped in the Leech pod (yelling FFFFFUUUUU...), during the explosion his vessel crashed somewhere on Helghan and there he wait for rescue (the commodore probably already went away in a similar fashion).
Rico (QI=0) and Sev, along with ISA survivors are baffled by the explosion, the nuclear fallout stop any transmission to and from the surface an the same for sensor, so they believe to have wiped out both the fleet and the entire Helghast population, we can assume they feel a little sad for having committed a genocide ...
So, everyone is happy for the victory and our heroes set back to Vekta, but since they are in simple fighters, i guess they will start a lon voyage home, hoping to be recovered along the way by someone (surely they cant tell to Vektans what happened on Helghan, because the combat vessels are designed for short range combat).
But why the Vektan surrendered to the Helshast? I can presume that this have been an imposition from the UCA (unaware of Stahl agenda).
UCA economy, already crippled by the loss of the lucrative black market of raw resources from Helghan, is about to collapse. The UCA treated Vekta as his lapdog, allowing him so deal with the Helghast question, but since they failed so clearly, losing two entire invasion fleets, they may have decided to "take control".
Nobody would bother Helghan for now, a ceasefire have been proclamed, so nobody would mind to ask them "hello... anybody there?"
I dont know how much time space travel take in killzone, even at warp speed, maybe only weeks or months, but somehow the ships carryng Narville and company will be recovered and brought back to Vekta.
And ... they discover something nasty, desperate in its need of resources and tired of the incompetence of the Vektan, the UCA have launched a full scale invasion of the planet, the outcome seems grim, since UCA forces are better equipped and have numerical superiority (and theyr ships outclasses ISA ones).
Sev, Rico, Narvile and the others will have to take back theyr weapons and, feeling the bitternes of having fought in a simple economic war, where human lives where considered as mere pawns, and begin to think that the Helghast, after all, may have seen things as they really were from the beginning...
So the main antagonist in Killzone 4 maybe will be the UCA, and finally we will see the return of Hacka, Luger, and the silent Natko.
Back to the Helghast now:
The entire irradiate petrusite loadout of Stahl flagship have detonated, exploding in the atmosphere and creating a massive EMP as well as a nuclear fallout on the planet, wiping out the entire Helghast fleet (except perhaps for the scout ship) and the space station.
On the planet, the entire petrusite grid, the petrusite mines and most of the engines have been linked in a mass reaction, exploding, we can think that probably a lot of Helghast died, maybe a third of the population, but only those unlucky ones that were on a train or next to a petrusite fueled engines during the event.
Howewer, Helghan population is massive and have a even bigger natality rate (a consequence of the short life span of the majority of the people) so they will soon recover frome theyr losses.
The Helghast are also naturally resistant to radiations (due to their conditioned cells), and the ubiquitous gasmask protect them from most of the hazards. Their bodies are also stronger, in the background it is said that they have efficient lungs, and their bones and muscles have developed an higher density to adapt to the higher gravity of the planet.
Probably, Helghan will be occupied for a while, by a civil war.
Stahl now have all the elements needed to rally the people and a part of the army to his cause, so he can:
Blame the council for seeking a peace with ISA (probably most of Helghan population want revenge, not peace after the bombing of Phyrrus and then of Helghan)
Scapegoat someone in his organizations and claim that what happened during his worldwide transmission was orchestrated by the council (highly probable judgin what happened in the scanner room).
Same for betraying the Helghan with their incompetence, allowing the ISA forces to nuke the planet after the "peace"
Its unclear why the Helghast had to steal the nuclear warhead (unless to use them as casus belli when they nuked Phyrrus) but since Stahl managed to develop in six months an incredible technology from the irradiated petrusite found on Phyrrus after Red Dust detonation, we can imagine what he could manage to do with an entire planet at his disposal.
The Helghast are shown as hard working people, and the planet itself is rich in raw resources such as metals, oil and everything needed to a growing industry, so we can assume that the damages suffered will be repaired, and soon the Helghast will recover and be ready again to wage war.
Meanwhile the council will be panicking, proclaming Stahl as a traitor, they will elect Visari daughter as new Autarch hoping to get the people favours.
The civil war will be like "the War of the Two Autarchs" or something like that
We can assume that Stahl will win, he is ruthless, cruel, power hungry and mad enough, making and ideal antagonist for the future.