They were thinking on a global basis. Cuba could have ceased cooperating with the USSR, which needed to maintain a "global presence" to look like a good match for the US.

Giving away missiles that were already there, unknown to the CIA, and not even concerned by the agreement would certainly have been a good move to keep the alliance with Cuba strong - IFF the leader was considered stable enough to consider them as a gift of goodwill to establish long term deterrence, and not something to be used within the next years - or even right now.

The guy must have mastered the art of negotiation to take them away - or to have given much more in return to Cuba that was required to maintain an alliance (ex: exports, money, ...)