Well yes and no...boot_the_grime is actually correct on this. The controversial plot points in S6 and S7 were either pitched or permitted by Whedon, as Whedon stated himself in various interviews. Noxon and Fury had some power, true, but Whedon did change things. He notably reviewed and changed the beating scene in Dead Things (made Spike's face less battered)
and he suggested the balcony sex in Dead Things and the invisible sex in Gone, per both Marti Noxon's commentary/interviews and Stephen De Knight's. Seeing Red? Whedon signed off on.

(I didn't have issues with S6-7, I actually like those seasons.)