If what you write is true they should have had clear warning about that coup attempt. It might have succeeded.
Or, the relevant intelligence agencies had clear warning, a good estimate of capabilities and what it would take to defeat it, and were able to intervene to assure that the Erdogan government was capable of putting down the coup
Or they had clear warning, sufficient intelligence about the intentions and orientation of the coup plotters that they were comfortable that the weapons would be no less safe even if the coup succeeded.
Or...
I would also be surprised if (besides initial instability) the expected outcome of a military coup is much worse than the status quo.
With the current situation there's probably not much good of saying "yeah, that place is pretty fked so we gtfo'd." Which exactly the message sent by loading up all your nukes and gtfoing at ~Mach 2.
Because they correctly perceive there's very little risk in remaining there.
* there's a list of 6000 people to be arrested, military and non-military, which must have existed before
* offensive on the ground took place at a time when they must have known Erdogan wasn't there
* they could have shot down his plane with F16s, but didn't
* the coup was generally terribly organized, in a country where the military certainly knows how to do it
* Erdogan is known to be a mischievous POS
Many people are sceptical and for good reasons.
Going with your suggestion would indicate that this safeguard no longer exists.