Okay, after wiki’ing it, we have, from left to right:  
Spike as St. Bartholomew.  
Pinkie Pie as St. James the Lesser.  
Starlight Glimmer as St. Andrew.  
Discord as either St. Peter or Judas.  
Rainbow Dash as either Judas or St. Peter.  
Fluttershy as St. John.  
Twilight Sparkle as Jesus, of course.  
Scootaloo as St. Thomas.  
Sweetie Belle as St. James the Greater.  
Apple Bloom as St. Philip.  
Rarity as St. Matthew.  
Applejack as St. Jude (aka Thaddeus).  
Big Macintosh as St. Simon the Zealot.
 
I suppose it makes sense overall.

@FuckyouImbetter  
Discord’s pose is similar to Andrew’s. It’s as if he and Judas have been swapped. The problem is that RD is not talking to Fluttershy, in which case she would obviously be Peter. RD = Peter would be quite clever, in my view: he denied Christ three times (RD is far from perfect and sometimes needs to be cajoled or tricked into realising what’s the right thing to do) but ultimately followed Jesus and founded His church (RD is Loyal to the end for all her imperfections).

Wait, is Spike James Minor or Bartholomew?

@PoemeMystique  
well 2 seats over from Jesus is Judas which is where RD is.

@dream-light-at-night  
So, the figures are not quite in the same positions as in the original painting, so it’s hard to tell who’s being whom, but Discord and Rainbow Dash are seated where Judas and Saint Peter are in the original. Appropriate (or ironic) positions for the Lord of Chaos and the Element of Loyalty.

@FuckyouImbetter  
Tbh it isn’t precisely parallel, so perhaps we are thinking too hard. (def Glimmer though)

@PoemeMystique  
@FuckyouImbetter  
“One of you will betray me.”  
“Discord.”  
“Discord.”  
“Discord.”  
“Discord.”  
“Oh, come on, I got all of that out of my system years ago! Besides, Rainbow Dash is the one in the Iscariot seat.”

@PoemeMystique  
no judas is discord  
oh wait I think it’s RD

The arrangement is slightly different, but Glimmer is identifiable as Judas. I approve.

@GaruuSpike  
Plus Twi is probably big enough for 2 normal spots

“Hello, table for twenty-six, please.”
 
“But Princess, there are only thirteen of you?”
 
“We’re all going to sit on the same side.”

pretty great! But should’ve had Rainbow next to Applejack doing some romance type thing

Da Vinci