Heresy and apostasy are not the answer to anti-Semitism
Do we really want Jesus Christ - who bled and died on the cross for our sins - to be ashamed of us?
We know from Hebrews 4:12 that the Bible is sharper than any two-edged sword, and discerns the intentions of the heart. We know from II Timothy 3:16 that all Scripture is given by divine inspiration and is profitable. It is easy to be ashamed of Scripture, but we should not be ashamed of God's Word. Christians are understandably leery of being perceived as "anti-Semitic," but that does not mean we can toss aside parts of the Bible that are politically inconvenient. So no, we absolutely should not stop reading the Gospel of John.
So, to address this head-on: The Apostle John was a Jew. The other Apostles were Jews. Jesus Christ was a Jew. The idea that the Gospel of John, the teachings of Jesus, or any other part of Scripture is a justification for ethnic hatred against the Jewish people is asinine and stupid. Refusing to read the Gospel of John is heresy and apostasy and should be condemned in the strongest possible terms.
Yes, it is true that both the Jewish leaders (the Pharisees) and the Jewish people rejected Jesus when he was brought before Pilate. They preferred to release a murderer instead of the Messiah who would conquer sin and death. It is a terrible tragedy that most Jews reject Jesus Christ as Lord and Savior, something the Apostle Paul mourned, writing in Romans 9:3 that he would be cursed for the sake of his kinsmen. But Christians today who were grafted in and have accepted Christ should take the Jews' rejection as an opportunity to realize that we also would have rejected Christ. Even the Apostle Peter denied Him three times. We should always see ourselves in the sins described in Scripture.
In closing, remember the warning of Luke 9:26, where the Lord Jesus Christ tells us that if we are ashamed of Him and His Word, that He will be ashamed of us. This ought to sober us and discipline our pride. Do we really want Jesus Christ - who bled and died on the cross for our sins - to be ashamed of us? May it never be. Remember Matthew 10:28, when The Lord tells us that we should not be afraid of men. The most they can do is kill our body, but God can destroy both body and soul in eternal Hell Fire.