What would happen if, for whatever reason, the US didn't notice the nuclear missile stations the Soviets were setting up in Cuba until they were already complete?
Waaagh, probably. Ultra-warhawks were egging Kennedy on OTL, so in this TL JFK probably does go along and drops the hammer.
Would they have been seen as a fiat accompli and become simply an angry piece of Cold War rhetoric now that both DC and Moscow were within easy range of nuclear destruction?
Not really. The missiles in Cuba were liquid-fuelled, meaning they needed
hours to prep for launch, during which they would be surrounded with extremely soft-skinned things (tankers) which go boom very easily (the missiles weren't emplaced in bunkers, due to lack of time, construction capabilities and space limitations) engulfing everything around them in a Flamageddon of Fiery Fire. Guess what would happen in those
hours (hint: it contains the words 'massive' and 'air'). Apart for those, the USSR didn't truly possess believable striking abilities against the US mainland (those would appear way in the late 60s, long after Hrushchov had been removed from power).
Would there have been a conference where both nations agree to remove missiles from Cuba and Turkey, respectively?
Hrushchov's endgame wasn't Turkey. He already knew (thanks to Soviet espionage) that the US intended to remove the Jupiters from Turkey on their own, due to their obsolescing from the US strategic inventory (it was all about solid propellants, baby, and the Jupiters weren't it). His intended goal was getting the US out of West Germany (and out of West Berlin).