Denaturation of compounds depends on the total environment and not just the pH and temperature. There will be interactions with other compounds that could be protective, which might be why it does not fully lose its color when cooked (but it does lose some in my experience).
The pH effects will happen in the beer no matter what, so there's not much to do about it. The temperature effects can be minimized by pasteurizing instead of boiling. If you do a regular cereal mash then you will end up boiling the wort for an hour as usual, which could be bad. It might be ok to do a regular cereal mash and add that wort to the main wort at knockout, I don't know. Since we know it still has color after cooking normally, that is my suggestion.
As for amount, typically it is 15% 2-row barley in a cereal mash, but that is then added to the main mash for full conversion. You will need to go higher than that for full conversion, or maybe use some 6-row, or maybe add some amylase. I don't know how much black rice you plan to use, but I would probably mash it 60/40 with 2-row (barley/rice) to get decent conversion. I would also probably whirl the rice up in a food processor after cooking to break it open a bunch, and then throw some rice hulls in the side mash.
And after tall that there's no guarantee it will work, but on the other hand it might be more work than necessary. You would have to do a bunch of experiments to figure that out.