How to describe "punishing" some text by making it less visible?

How about "obscure"? "v. To make dim or indistinct", "Not capable of being clearly seen, on account of deficient illumination." (Reference: Wordnik.)

Reduce font size, dim, grey out, camouflage (or blend), strike through, increase transparency...

Generically speaking, I would say these are all ways to deemphasize text, or to make text less prominent.

prominent: easy to see or notice; conspicuous

• penalize (when down-voted)
• obscure
• conceal
• hide (elementary but works surprisingly well)
• bedim (fits with graying-out)
• block
• flag (technical, usually for reporting abuse or attracting moderator attention)

The usual action is to strike the text:

strike, tr.v.

10. to remove words from a document, for example by drawing a line through them

If you simply want to mark the text as "bad," you can use one of a number of proofreading marks.