In my opinion, this fight needs more balancing. Same thing like Omega dragon, Warchief, Beast of darkness and Odracir. The chance/risk of loosing the fight and all your Creatures is to high, if i look at, how much time it takes to get those.
Anyway, at this moment of mod balancing, and i think you have nothing better than regular boss tier, i would try with two or more nearly maxed dodorex' with improved saddles. Go not only for melee, look for some Stamina and enough movement speed to run away, use your zombdodo minions. Try to fight him on an open area, were you cannot get stucked. Atack, and when he does one of his nearly oneshotting moves (seems to be a % value of your creatures life), flee, heal, and let the next take over. Always move, and hope not to stuck in his minons in a bad moment. Maybe it helpes if someone supports from air with a dragon if agro has to be switched fast to prevent one of you from getting killed. Spawn Silithia first to support the fight could also be an option. But even if you have Nephalem, this fight is risky with a high chance to die. If it's you private server without others, you can think about making a save before fighting, and rollback if you get killed - a little cheaty i know, but as i said - actually, the risk of loosing is way to high for the invested time before. First the Beast of darkness erases the omegas like dodos, but this guy is nearly untamable at the moment, because of it's insane damage output on vanilla settings.
Hope you make it, and always remember - the mod is still work in progress :-)

We were thinking of using a high level Broodmother and pump all HP and let him tank. Use the other bosses to deals as much damage as possible.

We havent even reached the point where the omega megapithecus calls his minions.

For Silitha, the Green Deity hasn't even spawned yet and the Omega Broodmother's torpor attack seems to stop our detox complety when 2 of us tried with 2 megapithecus

We killed omega brood with a dodorex and a dragon - no problem.
From the normal boss tier, Dodorex is the strongest with highes resistance. Megapithecus has way less hp, and even if you spend all lvls in hp, you might have only 150k more what is nothing in such a fight. I don't know, your server settings, everything i write is based on using wild dino lvl 120-150 and no changes on wild or tamed creature stats. If you have changed something, my ideas for the fight might be wrong for your settings, but good luck :-)

our server settings is mostly in vanilla with the exception of gather rate/taming time/growth/max diff 7 (max 210);

Ok we managed to do it with a dodorex and a broodmother. We finally got Bokito but we have no idea which stats to pump because it seems like he doesn't have armor

Nice, gz :-) The Primordials have higher resistance to compensate not having saddle armor, so that's no problem, but they spawn with fix lvl 7 if i'm right, so the higher your server's difficulty goes over dino lvl 150, the more useless is your primordial, because it doesn't scale with difficulty override actually. The only useful stat is damage and maybe a little stamina. You get not enough hp per level to make it worth spending level for this stat and the other stats are not necessary, primordials are fighters, so damage rules in my opinion. But be very careful, ultimate bokito, other omegas, psycho, odracir and beast of darkness can kill a primordial in seconds xD
And a last information:
No idea if you know this, but spawning a primordial is like a wild spawn. That means the stats were created randomly. It might happen to get bokito with 1000000 hp and 400% melee, but you also could get 500000 hp and only 100% melee and lots of lost levels. A huge diference, that you can't control, and this makes one primordial perfect and another neraly useless.
Hope in your case it wasn't to bad.