Well, if werewolves were such benign creatures, they wouldn't get such a bad rap nor would there be a Silver Hand. Note that while the Companions hunt the Silvers, the citzens are ok with them. No Jarl or other gives a task to croak them so they have popular backing. If the werewolves were regarded neutrally, then you could assume the werewolf ID in the middle of town & nobody would say boo. Try it.
As to how werewolves are treated by the Silvers, we don't know the why of it. Maybe those were captured after having killed a whole family of innocents or the Silvers are trying to figure out how to convert them back to human.
You never hear anyone mention the Silver Hand outside of The Companions, and the Jarls seem to have a problem with them in my game. Out of the 9 bounty missions I did, 6 of them were in Silver Hand locations, where the Silver Hand member was referred to as a "Bandit Leader" in the note.
Also, try going to the Silver Hand bases before you even get to Whiterun. They'll try to kill you. They aren't a group of paladins devoted to protecting people from Werewolves. They're bandits who also want to kill Werewolves. As Farkas said "Bad people who don't like Werewolves."
My guess is that the Companions were hired to get something back for someone that the Silver Hand stole, but finding themselves in a hard situation, the members of the Circle transformed and killed most of them. Survivors then regrouped and devoted themselves to getting revenge against them. This is probably when they adopted the name "Silver Hand," too.