I found something...:
You can get rid of all traces of the homebrew channel, and keep all your saves and purchased games. To do this, you’d need to back up your saves with the save extractor app (which can copy unmovable files like Brawl) and your SD card. Then, reformat using the Wii’s system menu. Insert Mario Kart Wii (or I’m pretty sure Brawl would also work) to update to 3.2. Then, use the twilight hack to run the savegame installer app directly, without installing the homebrew channel (I’m not entirely sure how to do this but I know it’s possible). After that you should be able to update to the latest firmware like nothing ever happened. There should be no traces that you ever did anything to your Wii (and thus your warranty would also be fine). Also, since Nintendo’s servers catalog what games you download using your system ID, you should be able to re-download all the games you ever purchased. Might need to double check on that last point, though.