I agree about the doctor advice. I've worn kilts for years (sitting at work, driving, hiking, etc) and have never experienced what you describe. Now, when settling in the car to drive I have to lift up my buddys to make it comfortable, but I drive a MINI so the seats aren't exactly those of a Cadillac. Point is, discomfort that you speak of shouldn't be happening. Where you wear your sporran at also makes a big difference (as mentioned before), as well as alergies (you want to make sure you're not having a reaction to the kilt fabric).
I go regimental whether wearing kilts or pants, so maybe it's just a matter of getting used to it, though the idea of a supporter is a good one. On hot days when I'm piping in public, I'll wear "bicycle" shorts that wick away the sweat, just so it won't run down my leg. I share that with you only as an idea as another thing to try (I wear Answer shorts, though MSR or any for that matter should help). It's just an idea.