First, we need to rule out Umarak, Brutaka, and possibly Vezon, since they're preoccupied with the whole "fusion thing."
Second, we need to determine if the Ekimites, Makutans, Karzahnians, and the Emanates are working together with the Matoran, or they're doing their own thing.
Thirdly, I just came up with a super-broken idea for the Fusion. What if Umarak, after stealing the Mask of Fusion and fusing with Brutaka, attacked Umbra and fused with him. Based on my description of Umbra's powers, he's immune to energy and is empowered by the inner darkness of nearby entities. And he also wears the Mask of Light. That would turn Umarak into the Kal of the Twilight (the concept, not the movies), and give a MASSIVE power boost to the fusion with Annona.
Now, to list the Kal:
Axonn: extremely good fighter, a natural leader for the Kal in a lot of ways. His powers don't help him in battle, unless his opponents try to throw feint attacks. He has a good chance of dying, but he'd put up one heck of a fight.
Hydraxon: immune to heat and water damage/immense pressure. His powers focus on repairing damage to objects and buildings, so he'd probably stay with the refugees. Could die during the Skrall's assault on the camps.
Keetongu: rapid regeneration prevents him from dying as quickly as others, making him the hardest to kill. Although, since he's a pacifist, he might die shielding a group of Matoran from Skrall.
The Piraka (nix Vezon): They haven't really been mentioned, but they could easily die in the siege. The only ones might survive are Reidak, Vezok, and Zaktan.
Kulta: reanimates corpses. Undead army vs. demon army. Nuff said.
Roodaka: mutation powers, not too good at combat. Might mutate Rahi into warbeasts, but she would be fairly simple to kill alone. She'd be in the back.
Sidorak: Rahi tamer, breeds warbeasts and can control them through advanced methods and his powers. He'd be in the back, so he has a chance of surviving.
Spinax and the Energy Hounds: adaptive biology and energy-tracking. They'd be a pretty good bet against the Warrior and Elite castes, though most of them, including Spinax, might die.
Krahka: shapeshifting, making her conceptually invincible. Imagine her turning into a massive dragon.
The Bahrag and Bohrok: mass numbers against mass numbers, so it should give the Matoran time to prepare or restrategize.
Kardas: massive dragon that shoots kinetic blasts, not elemental. Pretty much the trump card.
I omitted the Maxilos and Karzahnian Emanates since they're mostly confined to water.