So 50 percent of your country supports people who think all non Muslims should die, and you don't think that is going to cause issues when you go to non Muslim countries?
But crime is an individual concept. I may come from a family of criminals. Unless I commit a crime, I can not be discriminated against. The government can watch me more carefully, but they have to treat me like everyone else. This is a universal principle of human rights.
Even if 99% of Turks were homicidal maniacs, you can't argue that I am also one, unless you have reasonable evidence that I, "as an individual" may be one.
There are actually many details. For instance ISIS guys are sunnis. Some people that flee from them are alevites or shiites. These are different sects of islam. But from the point of ISIS people (or those that support ISIS point of view) alevites and shiites are not muslims. So again, who decides, who is to be classified as muslim? There are also christians in Syria. There are agnostics. There are people who call themselves muslims, but drink alcohol. There are people who don't call themselves muslims but don't eat pork etc. There is a whole spectrum...
So why waste all this effort to figure out who is a muslim and who is not instead of trying to figure out who poses a threat to France?