Turkey recognizes the jurisdiction of the European Court of Human Rights (ECHR). As such the ECHR is the highest court in Turkey. If the accused do not like the decision of the Turkish Courts they can appeal to the ECHR and let the European Judges decide who is guilty or not. Simple as that.
At least 4 die in clashes between PKK militants, security forces in east Turkey (Reuters)
from the article: Turkey indicts IDF commanders over Gaza flotilla deaths