Couple of points.
1. The primary evidence for Johannine authorship is external. For example, his authorship was widely accepted early on, and there were people inthe 2nd century that knew John and said he wrote the gospel, which is why it was accepted.
2. The fact that at some point some of Jesus' followers, the guy claiming to have been healed by Jesus for example, were put out of the synagogues in no way contradicts anything in the other gospels. That is a very weak point, and shows the weakness in the arguments against Johannine authorship.