Not necessarily. Ever played "The Witcher"? Geralt has the choice of sparing a werewolf because it was actually someone using their curse to hunt down the "real monsters", criminals and other bad folk.
Never played The Witcher, but that's a good point. However, I am basing my character off the Inquisition from Warhammer 40,000. (Not surprising, considering my avatar, huh? :tongue) If you know about the Imperium of Man in Warhammer 40,000, they are extremely intolerant of aliens, mutants and heretics and can be incredibly discriminating. Warhammer 40k does have some kind of werewolves in it, and some of them are tolerated, but only by their own brothers. I don't think the Inquisition will take very kindly to them at all, considering the Space Wolves themselves are already under scrutiny by the Inquisition.
That might be a little too much 40k stuff, so I'll bring it back to Skyrim. I definitely want my character to be more tolerant of these kind of things so as to prevent missing out on a lot of content. (Daedric quests, for example). However, I still want to do it in a way that it feels in-character. (Keeping away from the more evil Daedras, like Mehrunes Dagon or Molag Bal)
Do I have to become a werewolf eventually if I join the companions? Or can I rise up the ranks but not become one?
EDIT: @dannythefool I doubt I'd love it. I don't want to have built a bond with the guild and then be forced to kill them because of a roleplaying decision. I will probably go crazy trying to make a decision and waste a lot of time. However, I'm not going to stay completely away from them. I am certainly considering joining them still if I don't have to become a werewolf myself and if they are using their lycantrophy for a good cause.