1. As others have pointed out, the scripture applies to those called a brother. If someone was trying to remain in the congregation and was committing serious sin without repentance, then yes, they should be asked to leave the congregation. The behavior should not be accepted as normal within the congregation. As Jesus said, he should be treated as a man of the nations and a tax collector. That would mean "not your best friend". We all know that Jesus still spoke with tax collectors/sinners.
2. There is no scriptural basis even remotely for shunning someone who has already left the congregation. They left. They are now outside and that judgment is to be left to God.
3. Two things about the wording of "not even eating with such a man". First, if those weren't supposed to even be talked to, that wording wouldn't make much sense. Second, early Christians worshiped together at meals. Not eating with such a man would have the affect of not worshiping with him.
4. If you read the scriptures in John about not even saying a greeting, it is very specifically talking about "those who are trying to mislead you". It is referring to people who were actively trying to sabatoge their belief in Jesus' sacrifice. And again, if they were not supposed to be spoken to, then why say, "not even" eating with them?
5. The word for "not associate with" is the same word used in Thessalonians about disorderly ones. The same word, describing the same behavior. Yet, in Thessalonians it says, "but do not be treating him as an enemy, but continue to admonish him as a brother." Those two scriptures are describing the same behavior.
6. According to scripture a person should never be disciplined if they are repentant and want help to remain in the congregation. Jesus said you should forgive (in imitation of Jehovah) up to 77 times. Surely you might doubt someone's motives after 77 times? And yet, that is what Jesus is saying. If the situation is bad enough to be causing danger to the congregation after repeated incidents, then some action might be justified.
7. The reinstatement process as it currently exists is in exact opposition to the example of the Prodigal Son.
I investigated this extensively, because I really did want to be doing the right thing and I take the scriptures seriously. The way shunning is currently happening is, in most cases, absolutely unscriptural.