You are not completely describing the problem, nor the solution. Over a distance of a straight 5000m, Rupp may indeed currently be able to run it in a shorter amount of time than Farah, and even Soi, (since Soi has not run anything recent that indicates he is currently in 12:52 shape, while Rupp has).
However, the fact that the race is being conducted on a track where they are running in circles (instead of in a straight line the whole race) adds tactical requirements to be successful. Even though Rupp may now be faster than Rupp or Farah over a 5000m distance, what Farah and Soi bring to the table is the ability to more quickly accelerate (change gears) when running at 5k pace and sprint. They can't hold that top-line sprint more than 50-80 meters. But it is enough to get positioning and use the curves to their advantage.
Longosiwa also has that faster spring speed than Rupp, and that is how he got around Rupp with 250m to go in the recent Paris 5000m. But Longosiwa then slowed down (remember, they can't hold that sprint for more than 50-80 meters) to regroup for the sprint at the end. (Indeed Rupp, had to slow down to get around, but he eventually overtook Longosiwa by the end of the race.) When Longosiwa slowed down, two other runners (Soi and Alamirew) were coming on the outside of Rupp and boxed him in. Tanui came up too, and Rupp had to slow down and regroup to get around. The timing of the box with Longosiwa's sprint around and slowdown maneuver was quite unfortunate, if not planned (yeah, planned, in the sense these guys have a lot of racing experience and seen it all, and this was a classic overtake move.)
Since Rupp does not have that flat-out short sprint, change-gears speed to go toe-to-toe tactically with these guys, particularly since he is heavily outnumbered, then he needs to set up the race to his strengths, and the only way to do that is to flat-out run it wire-to-wire, at 12:50 pace. These guys with the sprint speed, but not in 12:50 shape, will drop. If they don't, then Rupp will make them have to earn their scalps for that race, while he comes away with the 5000m American Record.