So you want consequences, but you want them your way?
I think it was a perfectly valid design choice. You either take on this ability/disease and continue the quest, or you choose not to. I just think they should have closed the door. Currently, isn't it like if you say no they just say 'come back later then'? They should say 'oh okay then bye' and it ends the quest and you can never continue again, and it cleans it out of your quest log. Then it would be a closed off choice.
No, like that other poster said, consequence is about making a choice with repercussions from available options - not do questline/don't do questline. Not 'if you do this questline, this will happen and that's that'. If Bethesda employed writers, you could have had the choice to become a werewolf, the choice to decline but carry on with, as the other poster said, different treatment or challenge lycanthropy within the companions but maybe cause internal friction and perhaps even have to kill some of them. Clever writing would sometimes have a mixture of positive and negative consequences where you have to find the lesser evil based on what you'd like to happen. A great example is Veronica in New Vegas - nothing you can do gives her a great outcome, but you can give her the outcome you think is the least grim for her. That's clever writing.
It also makes no sense whatsoever (like so much of Skyrim's "writing") - other companions aren't forced to become werewolves five minutes after joining or be stuck with nothing to do.
A design decision was made to push the player to become a werewolf because Bethesda obviously believe players will think werewolves are cool and enjoy going on the rampage as one. That's why it's a superpower you have total control over with a negligible downside - a loss of well rested in a game where you level up fast anyway and there are multiple ways to grind experience if you want to - so it doesn't really matter.
I'd say vampires are handled better because they get benefits but definite downsides, so you have to think about if you really want to be one.