Well, guilds ARE a planned thing, just like cults. You mentioned ways in which they can hinder our forts, like secret cults often do in fantasy settings, but not ways in which they can help us. Lets remember for a second that this is Dwarf Fortress. We don't do things the easy, usual way, we do them the dwarven way. Let that thought sink in.
We don't just "kill" vampires. We often bury them alive inside their own personal palace to keep our forts from ever dying. Or we harvest their blood to create a caste of super soldiers. I don't see why an immortal being like a vampire, cunning and with a talent for persuation as they often are, wouldn't want to capitalize on the many ways it could help your fort without being killed.
Lets say a vampire arrives on your fort. He reveals himself as a vampire but your dwarves hesitate. He doesn't seem THAT bad a guy, and he's a pleasure to speak with. Your dwarves decide to keep him around, and set up a schedule so the strongest and fastest to recuperate let the vampire feed on them non-lethaly. With time, the vampire could become a noble, captain of the guard, protecting the dwarves that decided to look past his pale skin and blooddripping fangs and gave him a chance, or a legendary craftdwarf, or an object of workship. (something should be done about them no drinking alcohol on their own, or being able to enjoy the booze running through their victim's bloodstream). Something like that could happen with werebeasts too.
And the guilds of craftdwarfs. Those would be soo useful. Before departing from the mountain home to establish a fort near a volcano with acces to both fire clay and sand, your expedition leader sends a note to the guilds of potters and glassmakers to have those dwarfs be sent to your fort, not useless fishery workers and animal caretakers. Or maybe themayor sends the note through the outpost liason. Maybe in return for their help the craftdwarves the guild sent would demand to have better rooms than the normal populance, private dining rooms or statue gardens, andmaybe the guild itself would require you to send them a part of what the craftdwarves produced, free of charge. And if yourt fort becomes the mountain home, or successful enough, the guild could establish it as their HQ, and you could train peasants into proper craftdwarves to be sent to other forts (since sending dwarves out there to do stuff for you is going to be a thing). Of course, all that is the usual way these things happen in fantasy settings. Your stone haulers making their own guild and violently demanding living conditions on par with that of royalty could totally be a thing...
Well, those are my thoughts. Hope you guys had as much fun reading as I had writting.