Are there archives of telegrams or transmissions between Turkey and the U.S. during the Cuban Missile Crisis? What was the Turkish point of view on JFK negotiating pulling out the Jupiter Missiles in exchange for the USSR pulling out their missiles in Cuba?
A most interesting duo of queries you've posed. I will attempt to shed as much light on the matter as possible, but given the general lack of sources on the Turkish situation regarding the Cuban Missile Crisis as well as an actual historical omission of Turkey from many (if not all) of the telegrams exchanged between Khrushchev and Kennedy, this question is deceptively hard to answer without engaging in full "archive digging".
To answer your first question in a simple manner: no, we do not possess any solid archival information to suggest that the Turkish ambassador to the United States (or for that matter any Turkish official of government) was either pro-missile withdrawal or anti-missile withdrawal. All that we do have is the following from the NSA archives regarding the chronology of the Crisis in terms of documents and transmissions:
October 26, 1962 ---- 1:18PM: The State Department receives a cable from U.S Ambassador to Turkey Raymond Hare warning that Turkish officials will "deeply resent" any Turkey-for-Cuba Missile trade. Hare expresses his opinion that the most satisfactory resolution to the crisis would avoid the Jupiter issue altogether, but he suggests that if the missiles have to be removed it should be done gradually.^(1)
And that's pretty much it as far as my research and knowledge goes. Of course, we must understand that this lack of official communications between Turkey and the United States was due to the secrecy of the entire Jupiters-for-Cuba deal in the first place: if word got out that the U.S was negotiating to pull their missiles from Turkey, there is little doubt that NATO would further protest the move, giving the USSR a perfect bit of propaganda and (in the eyes of some revisionist historians), ending the Cuban Missile Crisis in a "win" for Moscow. However, I should note that if you're interested in other European nations' reactions to the Cuban Missile Crisis, consider investigating the Italian opinion on the matter next, as they were actually incredibly cooperative in facilitating a deal between the US-USSR.
As for the general opinion of the Turkish government, it's clear from the brisk (albeit limited) telegram from Hare that Turkey opposed the withdrawal of the nuclear missile systems. A main reason for this is actually quite logical: Turkey had actually paid for the missiles to be set up and their constant maintenance cost was being deducted from the Turkish government's budgets, see below for a State and Department of Defense report on the matter:
The group concluded that removal had several issues: 1) The missiles had just been set up for placement, committing Turkish money, which caused the Turkish foreign minister to oppose their removal because it “would be difficult for the Turkish people to understand” why their funds were spent without adding security to their borders.^(2)
We must also realise that this move by the US may have caused a slight (if brief) dent in Turkish-American relations, as Turkey felt that it was being "informed rather than consulted" on its own national security and foreign policy by the US.^(3) Even more critically, Kennedy and his administration feared that the loss of Turkish faith in the US caused by withdrawing the missiles would actually destabilise their relationship with NATO as well, causing them to be a potential target for future efforts of the Warsaw Pact (and more crucially: the Kremlin). Now in this case we do have a statement from a Turkish fellow to support that claim:
Turkish foreign minister Selim Sarper explained that if the installations were canceled before Polaris submarine substitutes were available, Turkish morale and faith in NATO and the United States would be undermined.^(4)
What's even more interesting however, is that some historians argue that Turkey actually benefited from being the "negotiating card" of the Cuban Missile Crisis. Ankara had agreed to deploy the missiles in 1959, but it seemed much easier for Kennedy to negotiate for their withdrawal than it had been for Eisenhower and NATO to agree to their deployment. What's more, when the missiles were finally withdrawn in 1963, Turkey enjoyed their replacement with the far superior Polaris SLBM (Submarine-Launched Ballistic Missile) shortly thereafter, not to mention the 2,000 or so technical experts that had been kept occupied by the obsolete Jupiter installations were now free to be diverted into other, more socially beneficial projects.^(5)
So that's my brief but hopefully thorough answer to your question. If you would a more in-depth look at this interesting viewpoint of a snippet of the Cold War, take a look at the work of historian Philip Nash, who has properly conducted an investigation into Turkish opinions during the Crisis.
Sources:
[1]: "Chronology 1: October 26, 1962 to November 15, 1962" (PDF). The Cuban Missile Crisis, 1962. The National Security Archive. May 14, 2011.
[2]: Nasuh Uslu, The Turkish-American Relationship between 1947 and 2003: The History of a Distinctive Alliance (Hauppauge: Nova Science Publishers), 135.
[3]: Quoted in Cody Fuelling,"To the Brink: Turkish and Cuban Missiles during the Height of the Cold War," International Social Science Review: Vol. 93, Issue 1 , Article 3. Originally found in, Philip Nash, The Other Missiles of October: Eisenhower, Kennedy and the Jupiters, 1957-1963 (University of North Carolina Press, 1997), 166.
[4]: Philip Nash, The Other Missiles of October: Eisenhower, Kennedy and the Jupiters, 1957-1963 (University of North Carolina Press, 1997), 98.
[5]: Cody Fuelling,"To the Brink: Turkish and Cuban Missiles during the Height of the Cold War," International Social Science Review: Vol. 93, Issue 1 , Article 3.