Well... im not a doctor, but there are somethings i know.
The THC is not a poison, nor its harmful to the body in any way, so there is not need to worry about it passing through your kidneys.
The only problem it would cause is that it alters the levels of water in the body... the cottonmouth is the most obvious effect of this. And low levels of water in the body can help the growing of kidney stones (dont know if its this your problem). But if you drink plenty of water, it should not be a problem.
Also, doctors usually exaggerates the told dangers of smoking (unless they were pro-MMJ), so if even they were not worried about it, you really shouldnt worry.