John 19:26–27: Woman, behold your son. Behold your mother.
Joh 19:35 And he that saw it bare record, and his record is true: and he knoweth that he saith true, that ye might believe.
How could someone even suggest John was not there???
I don't see how anyone could argue that the “disciple Jesus loved” is not John. John's Gospel is heavy on love, the word appears 20 times. John 3:16 shows God's love for the world and John by calling himself the disciple Jesus loved to show that God's love is persona. Not that God loved some more than others which would be the only meaning if referring to someone by that title in 3rd person.
We know all the disciples at one point fled, Mark 14:50, Matthew 26:56. I think there is little doubt John was there; it also seems that Peter too returned. Luke 23:49 clearly indicates there were a group of followers who beheld the crucifixion at a distance. The Romans crucified people in the open where they could seen by all as an example. The old rugged cross was far away from us, not the people in Jerusalem. It also took some time so the disciples could very easily have fled in fear and then returned in the crowd that gathered at the cross. I'd say the article wasn't written by a Bible Scholar.
I Peter 5:1 “The elders which are among you I exhort, who am also an elder, and a witness of the sufferings of Christ, and also a partaker of the glory that shall be revealed:”
Acts 4:20 Peter and John are defending their testimony of the resurrection “For we cannot but speak the things which we have seen and heard.” This isn't conclusive on it's own, but when viewed with other passages it certainly makes sense.