I don't think this "Paul contradicts Jesus" theme works with ppl who still believe in scripture as the word of God. Afterall, Jesus handpicked Paul as an apostle and clearly blessed him with holy spirit to do many great works.
Me personally, I do believe shunning to a certain degree IS indeed scriptural. However, it seems to me that nowhere in the bible is authority given to form a judicial system, a system with theocratic courts and judges and punishments/sentences. This would go beyond the statement given by Paul, and indeed beyond the attitude Jesus told his followers to have. (an attitude opposite to the pharisees)
Rather, the suggestion here is on an individual basis, directed toward all in the congregation. An idea closely related to the concept that "bad company corrupts good character", Paul is simply encouraging all Christians to avoid relating closely to any who 'claiming to be a brother practices all these things'. This would be up to the conscience of each christian to follow. Nowhere does it speak of a "state" of disfellowshipping which someone falls into after being declared "guilty of not repenting" in which they can't be spoken to for the rest of their lives until they follow some reinstatement procedure.This theocratic judicial system goes beyond scripture and intent, and ultimately I think does more harm than good to the Christian Conscience.
This same context also applies to 2 John 10 of "not even greeting someone who does not bring this teaching". Again, this is a personal recommendation directed towards individuals, a recommendation again closely related to the "bad company corrupts.." concept. Besides that, who is John referring to in this text when he mentions to not even greet? The context shows that he is referring to someone who refuses to believe in Christ, the "anti-christ". Can a JW say they are following this scripture if they shun someone that although in disagreement with JW doctrine, still believes in Christ?
For more discussion in the subject, there is always jwfacts.com.