Sounds like a cool game Dramacydle. I think using as much of the "40k Latin" as you can will help in making the setting feel more familiar to those accustomed to it. With that in mind, I'll try to drop a few ideas for you. Apologies if this isn't what you're looking for.
First though, a little clarification on the geller field: the geller field isn't used to protect the ship/station/etc in real space, for that you would employ void shields. The geller field is employed when the ship translates to the warp by putting up a bubble of "real space" around the ship to keep the demons and other denizens of the warp at bay. It offers no protection from debris, etc. So, maybe your players will eventually have to take down the void shields from the inside to allow for a better assault from space vessels. I suppose the geller field could be in use to keep the demon trapped in the cloister since it cuts off the warp.
Any cloister is bound to have a "reclusiam", which is the room in which the inhabitants (Space Marines, sisters, etc) display their relics and gather for ceremonies.
More than likely there would be an "enginarium", or engine room.
There would likely be training areas, or "gymnasia", for sparring, weapon practice ranges, etc.
You have to have an armory, because in the 41st millenium, there is only war.
Your sick would be tended to in the medical department, or "apothecarion".
The "scriptorium" would be akin to a library.
Some warp-twisted cherubim might be cool to employ from their cherubim eyrie.
Cameras could be replaced by servo-skulls.
The stations auspex arrays and other sensors would be centralized in the "Sensorium".
Your dining areas and kitchens would be part of the "refectory".
The station is likely to have several shrines or chapels dedicated to Imperial saints scattered about. If it was formerly a holding of a Space Marine chapter it would likely have a main shrine dedicated to the chapter's primarch and lesser shrines dedicated to chapter heroes.
A minor station formerly belonging to the Adeptus Sororitas would be a Sanctorum. Not sure if that could apply to any other Ecclesiarchy holding but I don't see why not.
Rather than a barracks, there might be a "rectory" for ecclesiarchy priests, frater militia, etc; there might be a convent for female orders.
Anyway, I hope this helps a bit. I have to hit the sack now I'll check back tomorrow evening.