It might just be my particular specialties in creature modding, but I find your first creature idea (flying animate sword, the pain in the ass would be making it even 1/20th as durable as an item without being too gamey) easier than your second (how realistic would it go and what kind of anatomy does a jellyfish even have?).
Note if you want contaminant attacks, having dangerous secretions on an attack that can grapple would be your best bet. If the jelly is super weak compared to attackee it just breaks grip and is affected by syndrome (unless onset is debilitating instantly). If jelly is powerful is proceeds to act like a wrestling GCS (Godzilla scale Jellyfish Megabeast?).
The sword thing actually works really well. The aura (which I repurposed into a spectral hand) is so incredibly fragile and not that hard to hit, since bodyparts can't parry. I had to give it massive natural sills in order to let it survive, so fighting it just relies on fighting skills more than equipment; I've had it get taken down in unarmed back in .34.
Regarding jellyfish anatomy, the creature I'm trying to make is heavily based off the Rutans from Doctor Who, which are green shapeshifting aliens which look like jellyfish because the original series had a tiny budget and plastic jellyfish are cheap. It's mentioned that they have to deliberately form vocal structures to speak, so the internal anatomy is pretty amorphous, hence why I'm leaving it as generic jelly, aside from a dedicated brain, which is just so it can actually resist blunt attacks. Except the brain isn't being rendered because "RUTAN:BRAIN:Unrecognized Material Token: RUTAN:Creature Tissue Material Failure: BRAIN:(no mat1):(no mat3):(no mat3)", whatever that means.
Anyway, regarding the contaminant, I didn't know there was a secretion system. Now I do, and it works pretty well. I still can't get the infernal brain to work, though. I'm not sure why it can't find the [TISSUE_MATERIAL:LOCAL_CREATURE_MAT:JELLY] token. It's spelled correctly and everything. In any case, it's irritating.