Sure, science is not a western construct but in the context of the final stages of the Ottoman Empire science over religion was considered a western value. This is not really a philosophical discussion, it's a practical implication of the decline of the empire and a political position in an attempt to reduce the islamic influence. This is a timeframe when people were burning observatories so that the "pervert scientists don't look under the skirt of the angels".

Atatürk was technically a dictator and a tyrant who executed quite a large number of islamic leaders in an attempt to curb the influence of religion. However, when contemporary Turks talk about being pro-Atatürk they mean the ideology of reducing the islamic influence on daily lives, education, judiciary etc. There are of course some people who would support extermination of religious people but those are just some crazies maybe you can find online and not a widespread position.

As you can see, the "Western values" in the context of Turkey are very specific set of ideals linked with the decline of the empire and formation of the republic and has nothing to do with the understanding of western values in other parts of the worlds or in philosophical sense. It's about practical implications on laws on marriage, inheritance, dress code, teaching the evolution Theory, funding of islamic education institutions etc. This is because Islam is not just something spiritual, it comes with instructions on governance -> the Sharia law.