Did Alex Mason kill JFK?

Solution 1:

There is no concrete yes or no to this question, but as you have mentioned in the question and @Timmy Jim said in the comments, the implication is that he did, but it is not confirmed anywhere.

However, a scene from Black OPs II seems to insinuate that he did not end up killing JFK. From the wikia:

However in 1989, when Mason is talking to Mark McKnight, McKnight asks about his brainwashing and Mason mentions that the Soviets "gave it their best shot", so it is possible that he was not involved in the Kennedy assassination and that his programming failed. Or it suggests that he doesn't remember what happened due to his programming so that Dragovich could have Mason carry out more missions.

Therefore, unless the developers outright say so one way or the other, no one will really know what happened and it is left up to the player's imagination.