We only did a daytrip to Kairouan from Sousse and took louages (Tunesian shared taxis). It was very easy to get one to go and return from Kairouan.
Kairouan definitely has the nicest Medina I have seen in Tunesia but the locals were really annoying. They're trying to sell you all the time carpets. I don't remember how many times they recommended us the carpet shop in the town hall.