Well, we probably would need to see if modifying the Disc Channel data could help, but if you want to play your discs without the filter you can launch them through USB Loader GX. Whenever the Wii changes into a different "program" the video mode tends to reset to default, so it's not usually possible to keep the deflicker from the main menu.
Whenever you insert a disc, USB Loader GX will have a disc-like channel pop up, and you can then play your disc without the filter, and whatever extra settings you want. So at least that's an option. For GC games, you can also launch your games through Nintendont with Force NTSC/PAL60 to have the filter out (not to mention improved frame rate compared to launch the games from the disc channel).