I don’t know if new players are having a hard time controlling, panicking, killing Scyllas or destroying Citadels,
but it is so simple, you get Redeemer (viral weapon) on missions, scavenging, or Disciples of Anu haven defence, don’t scrap those, just use , even without proficiency,
Also War Cry, LV 3 abilitiy for Heavy is super strong, almost paralyzing a Scylla,
so combining both you can lock a Scylla very fast, an example
This should be patched and Scyllas must become heavy resistent to virus.
Thanks for the tip, I used destroying limbs as tactis to make it panic, but now I see virus weapons work faster 
Was always wondering how to bloody capture a Scylla.
Went into a Citadel with Athenas and the team got owned. The Scylla has one billion hitpoints. Sigh.
How do you suggest dealing with it if it gets virus resistance? Especially if player takes strictly Any path without New Jericho or Synedrion technology?
You can get Hera HG pretty easy early game from Triton Poacher, with reverse engineering you get that weapon without Synedrion.
With enough paralysis that Scylla can’t attack or move very fast.
Also you can use War Cry.
You have also Biochemist perk, if you get one or two soldiers with that perk, Scylla is not a problem, because Orryx update is a mess
I’ve never thought about paralyzing Scylla with Hera’s. They don’t have much penetration, so you can only attack armour-stripped body parts.
I have this example, and I did it more times:
Well, even having 4 snipers with Heras and spare ammo in a great firing position it took ages…
You have actually panicked it with a MG Biochemist long before it was paralyzed. I would hardly call it an effective way to deal with Scylla =)
And having all haven defenders and all civilians killed or mind-controlled… Do you hold some sort of personal grudge against Synedrion? 
I always try to save as many people as I can in haven defense missions seeing it as a part of my job. Of course it becomes much harder to do with Scyllas present.
I thinl its not about hurting the Scylla. Its about paralysing it.
Let me see. A Hera does 7 Paralysing points each shot.
The lowest hitpoints a Scylla variant has is 3200. That means 320 Strength.
So…hmmm…320 / 7 = about 45 to 46 shots???
Well, in my last legendary campaign i killed 32 Scyllas and mostly of them i did not used virus damage… so just take risks and kill them with conventional gear and allowing Scylla to fight back.
Explosions first to destroy armour, after it massive gun fire in abdomen and head. If it came close enough use rage burst or a turret. If you kill lots of pandoras and have a priest in team you can also put Scylla in panic, with Pshicic scream you can remove will power also. With War Cry you limit Scyllas action points to half, so is plenty ways to deal with Scylla without virus damage that destroy one of the supposly feared enemys ingame. 
Paralysing needs to penetrate, so the weapon has to overcome the armor with piercing + damage.
Yes, you need a lot of Hera hits to paralyse a Scylla, but when you pass 1/2 of the paralysing damage she is pretty harmless because of the AP loss.
Just a little hint as spoiler: The Scylla Vivisection is only necessary for the Phoenix Point end, but not for any of the other.
I did not know that spoiler and is a very usefull information. Thank you MadSkunky.
Anyway, in late game, like it is now, is very easy to severe damage a Scylla and capture it after.
For more Infos: Sheepy's Tech Tree - wiki.phoenixpoint.com
I managed to capture a Scylla on a Synedrion haven defence with a team of 4 x Assault / Sniper with Hera pistols and 2 reloads each, 2 x Heavy / Sniper with Deceptor MG, 1 x Sniper / Infiltrator with Athena with 1 reload and a Raven with 1 reload, 1 x Sniper / Assault with Hawk.
The Scylla needed 390 paralysis as I hadn’t disabled the head which I think would lower the requirement.
2 heavies with Deceptor MG strip armour on the abdomen for biggest target and used war cry to reduce actions on Scylla for a turn or two. Avoid disabling legs as that induces too much bleed and will cause it to die before paralysis sets in.
Spider Drones were incredibly useful as a front-line so the Scylla & other enemies targeted them first, wasting their actions on destroying the drones as decoy. The triple deploy Spider Drones was incredibly useful.
I failed first Scylla on a previous mission as I only had 1 reload each for the Hera pistols and ended up with 328 / 330 paralysis.
Not sure how much virus was a factor because only one heavy had biochemist perk.
If one can take out the torso, that lowers the overall HP quite a bit, making paralyzing much easier.