I don’t think a student would be “punished” for skipping a grade. However:
- The OP admitted that the applicant will have fewer leadership positions due to graduating early. Only admissions officers at the colleges can assess how this will impact the overall application.
- There may be a concern about the maturity level of a student graduating HS early. Hopefully this can be addressed in the application process with thoughtful essays, strong LORs, solid interviews, etc.
Again, at this point the choice has been made. As noted above, it is important to craft an application list that includes reach, match, and safety schools that appear affordable and that the student would be excited to attend.