The article in your link claims that John's Gospel "contains many passages in which the authors condemn "the Jews" as sons of Satan and accuse them of murdering Jesus."
First, the word Satan is mentioned only once in the Gospel of John (13:27) and it is not in connection with any sons of Satan.
In fairness to John and other Gospel writers, the term "Jews" is used equally for the supporters and opponents of Jesus, and often to clarify (i.e. Jews and Samaritans or Jews and Romans), where a generic term "people" is too vague.
John does imply that Jesus' followers were banned from the synagogues, but that seems to be well disputed by some Jewish sources.
The link you provided also confirms, but doesn't qualify, that antisemitic policies of Christianity (official church) are vastly restricted to the Roman Catholic officials, and are clearly lacking in the Orthodox Church.
The pogroms mentioned in Ukraine also apply to that, since Ukraine was mostly under the Polish (Catholic) control. The reference to antisemitic pogroms after the Assassination of Alexander II do not represent Orthodox Church's official position. Most of Russian antisemitism stems from the Napoleonic wars, when (Polish) Jews in Russia opted to trade with the invading French armies while the Russian peasants killed all their live stock and burned their property (using Peter the Great's scorched earth policy) to deny the invaders any benefit of their blessings
The future pogroms were "justified" so as to deny the Jews in Russia the means to do business with Russia's enemies in the future, by having a portion of their live stock and farm products confiscated or destroyed.
Modern roots of Russian antisemitism are also not found in the Orthodox Church. Pro czarist groups and later emigres bought into the false "Protocols of the Fathers of Zion," apparently made up by the czarist secret police, as part of the "worldwide consipracy" of Jes and Masons "theory," something that was very popular in Europe at the time, and the fact that a disproportionate number of Jews, compared to their non-Jewish countrymen were involved in the leading positions of the Bolshevik movement (take for instance Trotsky).