Whatever the PKK did, that will not justify what Turkey did to Constantinople, Cyprus Greeks, Arabs, Kurds, and Armenians. Turkey aka Ottoman empire just has a very very bad history and something still going on today (illegal occupation of Kurdistan, Western Armenia and Cyprus), that it is far from a healthy country that US should consider it as an ally. Turks have also done too much against our Christian brothers many times in history, and they have yet to give the territory of Christians back to the Christians.
I've lived and worked with the Turks and you are correct...alienate them at our own peril. Most Turks are broadly pro-American, and hit pieces from Greek shills aside, they are close allies.