If you have access to Libris Mortis (The Book of Undead! And bad Latin!), the Necropolitan template is something you can slap on an NPC to make them into an Undead.
It's really just:
- Change their type to Undead.
- Give them Turn Resistance +2.
- Give them +2 on their saves vs. Control Undead.
- They still heal like a living creature, except they swap healing and negative energy spells (so
Cure Light Wounds hurts 'em,
Inflict Light Wounds heals 'em, etcetera.)
Swarms are a bit tough to deal with unless the party has access to ways to deal with them that aren't contingent on hitting them with big pieces of metal - I'd suggest hinting to people playing melee characters that a torch is more likely to connect with the swarm than their swords or axes would. As long as the spellcasters aren't solely rocking single-target spells (Swarms are immune to them, logically enough), they should be fine on that front.
Now, rat swarms cannot, by the rules, transmit Lycanthropy... however, that's kinda silly, and not AWESOME like turning into rats is. If you want to avoid the whole "LA +2 and extra animal HD harshly affecting the character and what the player wants to do with them" thing (which is a good idea!), may I suggest the following alternate rule?
When a character fails their save against Rat Therianthropy, they gain the Alternate Form (Dire Rat) class feature of the
Wererat Savage Progression. While transformed, their alignment shifts to Chaotic Evil and they become an NPC under the DM's control; the player must make a DC 15 Wisdom check to remember anything that happened while they were transformed.
An afflicted character that comes to grips with the fact that they are now a Wererat and works towards controlling their condition may take levels in the Wererat Savage Progression; once they take the first level, their alignment no longer shifts while they are transformed and they no longer require a Wisdom check to remember what happened while they were transformed.
As for Filth Fever... depending on the timescale of the adventure, it might not even be a concern. It takes 1d3 days to show up, and deals 1d3 Dex and Con damage; it'll be gone really quickly with minimal fuss if anyone has any ranks in Heal (1 rank in Heal and a Wisdom of 13 gives you a +2; if you Take 10 while treating a friend with Filth Fever, they will recover in 2 days without taking any ability damage.) Diseases in 3.5 aren't that nasty unless they are supernatural or otherwise especially virulent.