Given the severity of the political problems that scientists face in Turkey, academics need to become more politically involved — not less, as you suggest — to help bring about reform to the country's academic system (see Nature 500, 253; 2013).
There is no clear evidence to support your implication that the debate over the headscarf ban in Turkish universities has affected the quality of their scientific research. Other long-standing impediments are the real culprits.
Scientists in Turkey have had to contend for years with a lack of academic freedom and transparency in grant-review and faculty-recruitment processes. The small size of the academic community and a clumsy bureaucracy further obstruct the nation's research potential.
There are some notable successes, however. Contrary to your description of Boğaziçi University as “cash-starved”, in 2010 researchers there gained funding of close to US$13 million, of which more than $2 million came from highly competitive international sources (see go.nature.com/wik8xn).
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Aygün, O. Turkey's scientists can't ignore politics. Nature 501, 167 (2013). https://doi.org/10.1038/501167a
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DOI: https://doi.org/10.1038/501167a