I would definitely go with your doctor's advise on this one but a damaged kidney is indeed going to have trouble with protein. I know some people on a low carb diet in that situation who focus on fish and chicken as their "meats" and do not eat a lot of protein in general. They eat a lot of healthy veggies as their main meals, with healthy oils (tuna mixed with oil, oil & vinegar on salads, etc).
It is CRITICAL for your kidney to get 8+ glasses of water a day to help it work properly. I'd talk to your doctor of course but I imagine that's what he would say also.
So the water, nutrients, essential oils, lots of good veggies and fish are all parts of low carb that will still be good for you and your kidneys. There's no reason you should have to add sugars into your diet, or starches. The lowering of protein shouldn't cause trouble. Be sure to take your vitamins!