they'd have top MASSIVLY simplify the mission then as PVPers are a lot less prone to follow a script then mobs. given that you have to deactivate bombs in one of the missions, and another part requires you to clear NPCs away from civilians and tell em to beam up, it'd proably work VERY poorly under a PVP set up.
PVP combined with a story and objectives isn't a abd idea, but you'd really have to design the map carefully for it.
Klingon mission - to assassinate the captured hostages, fighting your way through any Fed rescue plans
Federation mission - rescue the captured hostages, fighting off Klingon assassination attempts
Winner of each stage gets NPC help at the next stage while loser gets to respawn with no help.
Final battle in the building decides assassination or rescue.
Too bad we can't do PVP Foundry or I'd be working on this mission right now.