I agree with you.IMHO, graying out text is a way to convey censorship. Allowing each individual to configure his HN experience sounds positive to me. I like reading controversial opinions just like you. For me, it's both a way to challenge my worldview and a way to understand a particular community better.
This has been discussed before (well, the general configuration for users). The main argument against it was that not having a common experience in the core elements makes it very hard for the community to stay coherent (which is given as desirable) and have good discussions.
Eg when I don't know how you perceive the comments in the vicinity of the discussion, it is harder for me to understand your comment's intentions and finer points.
Of course this doesn't apply to peripherical features such as the colour of the header bar.
