This would have been political suicide though, as the Russians would have taken this s a weakness on the Americans part, and they would have taken full advantage of the situation. Secondly, Kennedy could have ordered a full-scale military invasion of Cuba. But, this could have led to serious US casualties, and it would have not played in favour of Kennedy's political career. Further more, it would have undoubtedly had Russian casualties, which would have escaladed the situation higher, plus, the American chiefs-of-staff were not convinced that it would be successful either, especially as the offending missile bases were in remote areas and most were well inland. Confidence was also not very high, as the Americans did not want a repeat of the Bay of Pigs fiasco! .
Thirdly, Kennedy could order an air strike against the missile bases only. The problem yet again would be the Russian casualties and the Air Force was not sure it could deliver pin point bombings, on what were inland and small targets. Other options still lay for Kennedy as he could call on the Russians to remove the missiles, and explain to them, that their presence in Cuba was causing havoc for Russian and American relations. However the Russians, were highly unlikely going to listen to such a polite message, especially as they refused to even acknowledge they had missiles in their in the first place! The last option that lay to Kennedy was the option he took. Kennedy could pave a naval blockade around the island, quarantine it, and not allow any more Russian ships to enter Cuba. This would inevitably still leave missiles in Cuba, but the negotiations would continue in the background while publicly, Kennedy would be seen to be doing something specific. .
As Kennedy informed Khrushchev of these missiles, Khrushchev denied the existence of them, even though there was photographic evidence of them in Cuba. So Khrushchev was exposed as a liar.
