The Ottomans were fighting a war with the Safavid Shiites, and saw their own Shias as a fifth column. This is not new - Louis XIV exiled all the Huguenots on the same basis. The Catholics in England were severely suppressed, as were the Protestants in the Habsburg Empire - which triggered the 30 year war. 

The Spanish Habsburgs eliminated Islam and Judaism in Spain, to the last person. they repeated it in Italy and Portugal. The other Europeans restricted Jews into ghettos. Tell me, when did the Ottomans do that ?

Ottoman Emperors like Suleiman (the law giver) were very liberal, especially by European standards. When the Jews fled Spain, they went to the Ottoman Empire. the Orthodox Patriarch used to reside in Constantinople. No Muslim Patriarch resided in a Christian country. 

As for the definition of primary - were the Hutus of Rwanda the primary Catholics in the world? Could I say Christianity committed horrific genocides in the 1990s? If I include the Serbs, it is true.