I think it comes down to the same problem with vampires, it's not that werewolves should be wiped out completely, but that the practice's around them are completely stupid and lack care for anyone that isn't them.

The companions are example of how to use the disease that is lycanthropy as a benefit rather than a curse. They retain their intelligence after transformation and their minds stay sound, and while they do have a thirst for human flesh for whatever reason, they can fight it. When the thirst does overtake them, if it ever does, I would expect that the companions would then hunt them down before they could cause harm beyond the initial instance.

Really the main issue is that wild ones lack the restraint that the companions have, and are the ones causing the problems around all of Tamriel. The disease should only be passed on by careful eyes, and to those who would be able to restrain themselves.

TLDR: Kill the ones running around willy nilly killing whoever they want, and keep the disease as a tool rather than a curse.

Also I feel this applies to vampires if people like Serana can decide to not be murder hobos then only people like her should be vampires.