Obsolescence was the public justification, If I remember this right the Jupiter’s were liquid fueled. Solid fueled missiles plus SLBM’s were coming online. However, from a technical viewpoint the Jupiter’s were still superior to what the Russians were deploying in Cuba. So, in the trade the Russians got a slightly better deal. To keep the Camelot\Kennedy mystique going the press painted something different and the public swallowed it.
Even the author of the Politically Incorrect Guide to the 1960s, Jonathan Leaf, made it very clear that ultimately, even without the CMC, removing the Turkey missiles would have inevitably happened since they were obsolete due to nuclear subs. And if you read that book, you’d realize he’s no JFK fan and generally paints JFK in a very bad light overall.