Well it's not like they're blurring the guy out of the DVDs or anything. He was present in the Elimination Chamber DVD, for instance. They're just not going to include matches with him where it's not absolutely necessary, like say on an Edge DVD.
I have never bought a WWE DVD, so I have to ask: what does WWE do with matches, shows, or highlights that include Chris Benoit? When Wrestlemania 30 comes and they release some massive box set of blu-rays to commemorate it, how do they handle Wrestlemanias 16 thru 23? Surely they can't just completely ignore Wrestlemania 20's main event or the first Money in the Bank ladder match at #21. At least with Eddie Guerrero, they don't completely ignore the man's existence, but obviously they have some understandable trepidation about Benoit's inclusion in their releases.