Yoga is great for stress relief, especially the meditation part of the pracitce (known as 'savasana'). This would then help any stress-related kidney problems.
Also, many yoga poses involve toning the abdomen & the inner organs, such as twists, inversions, and core strengthening poses.
But yes, definitely check with your doctor before beginning any major exercise program. Yoga is fantastic but, as with any health care, it can injure you if you don't know what you are doing.