Extremely late reply, you probably found out already....oh well.
1) Try and improve public health by building sewers and baths, normally I would do this once the population ahs grown to 4-6k.
2) If there is a plague, seal the city off! No units inside the plagued city should leave for another city.
3) If your family member has been affected keep him in close watch, once your settlement stops having a plague, remove him from it (so you have max. benifets of his skills during the plague) and keep him a short distance from the city, so the city won't cathc another plague and he can be in close proximity in case the settlement is attacked. The plague would wear off overtime, but your family member/agent can still get killed in the process.
You should be cautious of attacking Macedonia early in the game (can't remember, maybe 15-30 years into the game) since a plague normally appears there. Egypt and Carthage have pretty fast growth, try and invade them early in the game and control the plague. Nothing can be worse than not knowing a plague is in the city and you send your best general and troops to overrun its defences :x .
BTW, mercenaries rule, they really make campaigns shorter
Edit: I realised how irrelevant the message I quoted was, this message is a reply to the topic about plagues.