Yes, the gray-ification of EVERYTHING in OS and in Safari is giving me headaches, too. It is another example of the problem of elevating Ives' into the UI realm. What is sleek in hardware is not sleek when you are trying to read a finder list, information in the App store, and web pages that inherit the Gray Font Mania via Safari.
The only solution I have found (for websites) is to use FireFox for the Mac.
Go to: Firefox > Preferences > Content > Fonts & Colors. On websites that don't build in hard-wired fonts, I use Helvetica 12 pt. and a true black color. Makes some of my headaches go away.
Good luck trying to get Apple and Ives behind the idea of readability...