What you say may very well be true. And many parts of the Gospel of Judas may also be true. There is not that much contradiction.
John appears to be the least reliable of the four accepted Gospels, and had an agenda of marginalizing and insulting the existing Jewish community. Mark was completely neutral about Judas, and it is believed that that Gospel is the most authoritative and earliest version of what really transpired.
Well, I simply refuse to believe that Jesus knowingly asked Judas to betray him as suggested by this National Geographic program.
It just doesn't make any sense at all.
I believe the word of Matthew, Mark, Luke and John over Judas any day of the week.
Given that Easter is here, I suspect that this program is yet another attempt by the MSM to distort Christianity and thus dishearten its believers.