The West Wing was shot on film and six of the seven seasons were broadcast in high definition. Warner Brothers made all seasons available in high definition through download and streaming, but the plot recap and opening title sequence are in standard definition. Why?
In addition to the reasons jlmcdonald stated, I think part of the logic might be that sometimes the pilot recap contained scenes from the first season, even in the later seasons of the show, and rather than go back and forth between SD and HD in the same scene, keep it all SD.
A few years back HDNet started airing Cheers in HD, transferred from the original film sources. It looks great most of the time but occasionally an episode looks horrible, sometimes certain angles of certain scenes look horrible, and I have to think it's because sometimes high quality film sources for certain episodes and scenes are not available. When it occurs in the same episode it's pretty jarring, so I would think they would want the recaps to just have one consistent look and feel.
This is just a possible guess, but it's likely it has something to do with the process needed to create the plot recap and the title sequences. I imagine the cost-analysis showed that it wasn't worth it to recreate those from the original film source (they'd have to re-edit, re-cut, re-mix the audio, etc.). They also didn't do anything with the audio when releasing the HD downloads, leaving them stereo only. Saving a bit of money (and bandwidth because your resulting digital files are now a little smaller) on things that people probably don't care much about when watching a show online can add up in the long run, especially knowing that a measurable selection of the viewing population would be using laptops, mobile phones, tablets, etc. where the difference between 480p and 720p (which at least Amazon Instant prime is ... don't know about iTunes) is not very noticeable.
If they ever release a Blu-ray, Warner Brothers might make different choices.