Agreed, even if you have some oddball situation like As4s* against 8s3s* and a flop of 7s 6s 5s giving player 1 the nut flush and player 2 a one-outer (9s), it's still the same EV running it once or twice.
Running it once gives the pot to player 1 if anything but the 9s is dealt in the next two cards, which happens (44 / 45) * (43 / 44) = 43/45 of the time.
Running it twice means he scoops if anything but the 9s is dealt in the next four cards, which happens (44 / 45) * (43 / 44) * (42 / 43) * (41 / 42) = 41/45 of the time. They will chop the pot the remaining 4/45 of the time, meaning player 1 has an additional 2/45 EV when that happens, giving him a total EV of (41 + 2) / 45 which is exactly the same if they ran it once.
Conversely, player 2 gets the whole pot running it once 2/45 of the time, and half a pot 4/45 of the time running it twice, giving him the same EV (of course).
Only difference running it twice is that player 2 has a better chance of winning something, but he cannot scoop in that case.** Same EV, less variance.
* My initial scenario was not quite correct, corrected now.
**Edited this sentence to make it correct and clearer.