Not really, since there's no secrecy or cooperation.
You just decide if you wanna join one side or the other. If you join the cultists, you don't research. I think I'd re-use most of cult-code to do stuff, but you'd get your spells from the get go. Maybe start with a simple offensive spell (summon a 20 force mellee weapon at any time by converting a metal rod) and you can sacrifice people or animals to earn 2 more spells.
The thing is: the more people join the cultist side and the more spells/sacrifices they cast, the faster the round progresses and the sooner the Great Old one shows up. No coordination required, just go forth, kill shit, sac them and spread the joy.
For cosmetic and clearly cultist-revealing, I'd add a "madness aura" to cultists. those weird things that happen in the first stage of the round? They happen very frequently around the cultits (7x7 around you). That means wherever a cultist goes, lightbulbs break, blood appears out of nowhere, gibs, floor tiles break, the station slowly unravels itself.
I think I'd had some kind of wisps or floating fire to still keep some sort of lightning around the station.
And I think I got a good counter for the non-cultists. First and foremost, they should grab weapons and shoot cultists. Obviously.
Killing all cultists doesn't end the round, it just gives you more time.
Cultists can't use weapons. Most items they pick up should dissolve or malfunction. They'd have to rely on their spells and rituals.
Now the core of the game is escaping the Great Old One or killing it. Killing is easy: I'd code-them to be exactly like Nar'sie (they'd convert tiles to the cult tiles) but vulnerable to bombs that are powerfull enough. No welder bombs, but anything else goes. So that's one way. You'd have to figure out where the Great Old one will spawn to get an advantage.
To escape you can't just call the shuttle. That'd be disabled after the round reaches stage 2.
You need to create a portal to escape back to Centcomm. This portal fries cultists that touch it but otherwise lets crewmembers escape. There's 3 ways I came up to assemble that portal.
Cargo will have a new option to buy a crate carrying one of them. This would replace the entire cargo menu with a simple message (Take this, from a friend…)
If cargo is flabbergasted, you can modify the teleporter in science. To do this, R&D can print out a circuitboard. The R&D console gets changed to a screen that just says it's malfunctioning with a single button "Create" or some foreboding thing. Use the circuitboard on the teleporter and that will modify it.
The other way is the gateway. It will stop working when the round enters stage 2. You can activate it however and it will be warped and twisted into a portal.
That's where the conflict arises. No matter the method you pick, the cultists will be notified of a portal on the station. The portal will need charging and charges faster the more power it's connected to. Got singulo wired to the grid? Congratulations, you'll be safe in 30 seconds. Shoot cultists in the meantime.
Power is gone to shit? Fix it, get a Pacman or start praying.
As a last option, when the Great does show up, a "friend" will open a portal in a random point on the station and broadcast a warning. You'll have to rush there and enter to get saved, but that requires dodging the Great One and the cultists.
At the end, you get a report on how many cultists they were and how many people survived.
We can also make the cultists powers thematic with the Old One that will spawn.
How's that? Let's people counter one another, progresses into larger and larger shit, it's a garanteed clusterfuck and there's no autistic "let's hide in maintenance slicing wrists for 15 minutes before stun-talisman'ing someone and then calling golems non-stop for 15 minutes"