I would venture to speculate that there will be Werewolves outside of the Companions. There have been Vampires outside of the "Main Vampire Quests", I don't see why this will be any different. They may not show up until later levels but Werewolves are human during the day. We could be talking to them in town and never know about their nightly shenanigans. Unless we follow them and find out...
I imagine the fun in destroying werewolf dens - actually, wouldn't werewolves be crazy OP? Which means making a den of werewolves would be...extremely challenging. However, with logic such as this, you could become a werewolf outside of the Companions, yes? For instance, in Oblivion you could become a vampire via involuntary infection OR via Vicente Valtieri.