While I mostly agree with this, it is a very common convention to show additive text in green and destructive actions in red, when I saw the yellow blue version I have to look for a key to see what it meant, I worry that we're making the users think too much. You should have IMMEDIATE understanding of what the colors mean and not have to think too hard about it. While some users could see the red and green as a value judgement I think its common enough in diff views in other products that I don't think it will be an issue for most users, especially user new to the system, but familiar with the pattern elsewhere.
second issue; colorblindness. The mediawiki.ui colors are actually tested against a color blindness simulator to make sure that the green has enough blue, and the red has enough orange to differentiate them. These colors were not arrived at accidently or on a whim. If for readability sake we choose to use a lighter shade of those colors we should make sure those values of the color are further tested against a color blindness simulator again.