Clearly not. Since Europe has gone secular, it has been more peaceful. There has not been any wars between the Catholics and Protestants in many, many years.
Now about the Muslims in eastern Europe, from what I understand are mostly secular and liberal types. So, I don't get the fear of the Albanians, Bosnians, Kosovoks (is that what they're called?).
But I do get the fear of Turkey because many Turks are conservative, especially in the mainland, not Istanbul. Also, in my opinion, I really don't think Turkey should join the EU because only a small part of it is in Europe, while a large part is in west Asia. Geographically, I don't think Turkey is part of Europe.
I don't think that's the reason why some don't want Turkey in the EU. Let's not forget that Greece, although it has the size and population of Portugal, it has one of the biggest budgets in defense. Why? Because it has a long-term conflict with Turkey.
Central Europe doesn't want Turkey in the EU... Now. Because most of Europe has christian-democrat/conservative governments. Ask what was these countries' opinion about letting Turkey into the EU a few years ago when the governments were mostly social-democrats.
Many still think that Turkey should enter the EU, specially now. For two big reasons. Turkey is called by the european economic/finantial press
The Sleeping Giant, because it represents a huge potential of export market and production (the same way eastern Europe represented 20 years ago), specially for countries whose economy depend a lot on exportable products... Like Germany (the country that, curiously, has been dealing with an immigration issue of people coming from... Turkey) for example.
The second reason is related with the revolts of the Arab Spring. These countries are very vulnerable now to all kind of extremist or totalitary regimes. That's what represent a threat to Europe. Europe doesn't care if they're islams or not: the north of Africa is a huge market for economies like France and Spain and it still have huge potential to explore.
So, Europe want to keep these countries with revamped regimes with friendly relationships. There's where Turkey comes in, because Turkey has been gaining a very big influence on its neighbour islam countries in economy, finances, but mostly, in diplomacy.
The last thing that Europe wants now is these countries to create a political/economical bloc like the EU is and that represents direct competition in a moment of weakness for the EU.