I think we could have a whole new cult to play as in Space Station 13, something inspired by The Conversion Bureau.
 
Custom map that replaces Lavaland with a section of Equestria, with some of the monsters seen in the show that are just hostile to everything. Includes locations like Ghastly Gorge and Everfree Forest.
 
Cult of ponies trying to turn enough people into newfoals (and griffons, changelings, hippogriffs, yaks, buffalo, zebra, etc. It would be a random chance thing.) so they have the numbers to search the dangerous ruins and caves for an artifact that can hurl the space station into the sun!
 
An alternative win conditon could be converting everyone into a newfoal; or at least those in charge. Another option is boarding the station and getting that nuke disk, but stealthy infiltration would be right out unless you have a changeling player; and your team can only get a changling by chance from making newfoals. If you do get turned into a changeling you have a lot of options if you change the AI Laws to declare ponies as human, or if you sneak into virology and turn a sample of ponification potion into an airborn ponification virus.
 
There is always the chance that Space Station 13 will have to be evacuated for reasons completely unrelated to ponies. If you have never played Space StaStaion, know that calling the emergency shuttle to the station is almost a matter of routine in this game, usually related to an accidental explosion following an escape of the slimes, the monkeys, or even the bees or spiders. That leads to a win by default for ponies.
 
Station can win by finding the artifact and sending it off world, or stealing it before the ponies can finish activating it. Alternatively, the Station can kill all opposition, or robotics can build enough mining bots to outnumber ponies 10 to 1 and stripmine 80% of the ecosystem.

“OH FUG NUKEOPS” -Greytide-Pone