There a few facts that some here seem to have missed.
1. The obligation to discipline emanates from the mitzvah of hocheyach tochiyach. The mesilas Yeshorim spells out that this mitzvah is hinged on the outcome. If rebuke has positive effect, then doing so fulfills a mitzvah. If it causes a backlash, then the mitzvah is to remain silent. Our chinuch systems appear hell-bent on doing something, otherwise it is tantamount to approval. This premise is faulty. Meanwhile severe forms of punishment, or those unrelated to the “crime” teach nothing and usually backfire. Such “dsicipline” is actually abuse and not al pi Torah.
2. It became recognized many years ago that the OTD kids were being mislabeled as “drop outs”. Actually, they are “throw outs”, and there will be much to pay on Judgment day for the spiritual murder of these neshamos.
3. Yes, Emunoh issues are excuses. However, the questions are generally legitimate, and deserve answers. One main reason our “system” bases severe rejections on these “questions of faith” is because we (the system) don;t have the answers. If any mechanech(es) would try to answer the questions on Emunoh as they would about nuances of current questions in Hilchos Shabbos, they would discover their own real issues, or perhaps save a child from slipping into the abyss of OTD.