No, didn't view it as condemnation at all. My response was due to a couple things. One, some people feel the restrictive diet punishes in that you may have to take away a favorite food. We did have to do that, but my wife had the time and patience to learn how to make alternatives that she ended up liking quite a bit.
Some people fear the diets because they are afraid of lacking nutrition. You do need to be aware of which diets may end up naturally being deficient in certain things, and you need to make an effort to include those things (like calcium or perhaps D in CF).
The biggest concern of mine when talking about diet is effort. Many people don't do it because 'it's too hard', and they don't want to spend that amount of time in the kitchen. Some allow a level of cheating ('one piece of pizza won't kill him/her'), which defeats the purpose of the diet entirely.
So the 'stress to the child/family' objection your doctor offered is the weakest of the usual objections, and if you really wanted to try diet your doctor likely wouldn't object.
In our case, daughter had diarrhea and loose stools for almost an entire year, every day. We started on SCD (Specific Carbohydrate Diet), which was originally designed for Crohn's or colitis patients I believe, and within a short time (weeks maybe?) she started being entirely regular.
We all (wife, daughter, me) did the early part of the diet together, so when we sat down she was eating what we were eating. First few days was basically broths, then it gradually introduces easy to digest foods (well cooked meats and certain vegetables). Her stomach has been fine ever since. We're not still on SCD, but we still eliminate several things as I mentioned before.
If you want more details on anything about my experience, my email is in my profile.