Who is supposed to call? The runner essentially takes the place of the injured batsman when it comes to runs, so if it was originally the call of the striker to run (say, a single to mid off/mid on, where the non-striker should not be ball-watching) then the runner makes the call. If the non-striker was to make the call then he would as usual.
Of course that never happened in the real world. There have been instances where there were two runners on the field and all four men ended up at the same end since even injured batsmen have the natural instinct to run. Runners are confusion.
But great fun.
Bring the rule back, please...even amended. Hell, make it a Twitter vote if you want to. #ICCCricket - "Should Batsman X be allowed a runner? 3 minutes to vote now!"