When granting the charter school its charter, the state must have agreed to some funky arrangement about language credits. That’s between the state and the charter school. It would not concern a college; they don’t care at all about the specific arrangements or hoops the charter school had to jump through. Colleges want to see commitment to stick with a language to a fairly high level, and many will care about the habits of mind that are cultivated by language study.
Turkish is a language with a fascinating cultural and political resonance, and of course a college would find it unusual and interesting. It seems that a year of another language will be necessary to satisfy the state requirement, but if a fourth year of HS-level Turkish is also available to your kids, that would likely be interesting to colleges.