If anyone knows any mods that fix these issues, post them here.
http://www.nexusmods.com/skyrim/mods/22650/? (the full version) fixes the werewolf issue.
Although, Marss, three of the companions are (possibly) looking for a cure for lycantrophy. And only a select small group within the Thieves Guild actually serve Nocturnal. At least with the Companions, you get to choose to cure yourself later if you so prefer.
I have the same issue with many of Skyrim's quests - almost invariably you are required to do something basically evil to do the quest. The daedric quests are the worst. I'd love the conversation options to say, WTF, no way will I... (bash his head in with a mace, sacrifice my loyal follower, murder my trusting followers to improve my sick weapon, murder some deranged old chap in the cold wastes, etc. etc.)
And what about killing someone who is living a life of repentance, helping the very enemies he once terrorized?? With no option to say to the Blades: NO WAY you narrow minded moron, without him we'd all be dead!
Fair enough, but there is no option to decline these types of quests. It pretty much auto starts, and jams up your quest log.
I craft/enchant better weapons than any of those so-called "artefacts", so the descent into evil isn't really that tempting.
I'd like to be able to exercise FREE WILL, which is really missing at times in the Skyrim universe.