No, it’s not “Him contradicting Scripture,” but it is you selectively quoting Scripture!
Let’s look at the whole sentence, please: “Truly, I say to you, among those born of women there has risen no one greater than John the Baptist; yet he who is least in the kingdom of heaven is greater than he.”
Jesus is making a distinction between those who, while living on earth, will have seen the Kingdom of Heaven established, and those who did not live to see it established. Among those who did not, John is greatest; among those who did, all are greater than he. A couple of things are important to note, here:
[list]*]The notion of ‘greatness’ here doesn’t denote any personal quality of an individual, per se; rather, it seems to indicate a greatness in what a person has experienced – anyone who experienced the ‘kingdom of heaven’ is “greater” than the Baptist.
*]John died prior to the inauguration of the KoH; Mary died after it. Therefore, Mary is “greater than he.”
*]It does seem that Jesus is talking about John as a prophet, so it’s probably not unreasonable to suggest, also, that status as a prophet is meant here: John is the greatest of all the prophets, but even the greatest of the prophets is not greater than those who lived to see the messianic prophecy fulfilled.