The Aurobindo Society that runs The Mother's Inetrnational School also runs a school called Mirambika, which follows a free progress model of schooling. Since the school did not get CBSE approval for Board Examinations, all the children move into a regular school from class VIII. Some parents move the kids out sooner.
Now, my son's best friend is someone who spent 6 years under that system and joined mainstream Mother's International School. He is a wonderful, sensible, sensitive boy who has done and continues to do rather well academically too. The other students from his batch who joined mainstream schools have also all done very well. In fact they are all brilliant students.
Did they have any adjustment problems - Yes they did. But point is they all overcame them successfully and went on to handle challenges in life with an amazing confidence. They wouldn't trade their time at that school with anything else. It was one of the best things that happened to them.
So the point is when ever there is a switch from a certain environment to another, there will be some angst and heartburn. Even if the switch is from an Army School to a regular less disciplinaruian school, there will be some adjustment issues of a different kind. Within the same system of schooling, moving from one branch to another, or change of one subject teacher to another can necessiate adjustments.
What is important is to see the issue in a holistic manner. While it is important to provide children with a certain stability, it is also necessary to give them some challenges and lessons in adjustment and coping. Any method that allows children in their younger years a lot of freedom and latitude and gets them interested in learning is good for them in the longer run. Just because they may have to get into a different system later is no reason to deprive them of the goodness of it in the formative years.
Plus, as parents we need to continue providing the balancing inputs in their life. If there's too much discipline in school, we need to give them opportunity to break free and vice versa! Some checks and balances will have to be put in place, no matter where they are!