With Cassarae's Class Quest looming overhead, the Florineth would have to be dealt with one way or another. But destroying a family didn't mean killing every single living being that was among it. If that was the case, when Cassarae got the Quest to take down the United Coalition of Terranova, she would have had to kill both Sylas and herself since they were both born and raised in the nation.
No, Cassarae's Class Quest only demanded that the structure that made the target, well… the target, be taken down. A certain percentage of its leaders and important structures had to be cut down and erased.
But the irony of it all was that the reason the Florineth had become a target for Cassarae was because of Nyssa. Cassarae was most definitely a very jealous wife, and she didn't want anyone near Sylas.
By the same token, though, Sylas couldn't just let Cassarae kill Nyssa just because, while he also didn't actually care what happened to the rest of the Florineth.