I do realize this. I also know someone that has had problems with it on github's diffs. I do think it would be better to use other colors to avoid the issue entirely.

Do you map a 3D scene into 2D without any information about which aspect of the scene is important?

So you propose that colorblind people should make their OS turn all images, photographs and video into false color not correlating with reality because in some specific contexts color is used symbolically and it's important to distinguish between two colors? One option that might work would be a special drawing mode implemented in the OS graphics stack that did some mapping depending on what's configured in the accessibility settings; then applications could request that in the rare cases where it's important.

That's a really interesting idea. You'd want a fast toggle for it, so that you could use it primarily for browsing semantic content that uses colors, but not always for photographs or videos that represent the real world (unless those photos or videos contained such semantic content). It's not ideal, but much like assistive devices that translate vision to other nerve impulses (http://www.nei.nih.gov/news/briefs/weihenmayer.asp), it could be useful as a learned adaptation.

That said, it would also make sense for diff software in particular (as one of the most prominent software uses of red and green right next to each other for semantic purposes) to have an easily adjusted option for a different color scheme for the very common case of red/green colorblindness.