I think Mikoto beating accelerator wouldn't have changed anything. They'd just redo the calculations even without tree diagram they would conclude it would be within acceptable margin of error and continue.
What Mikoto has to do is nothing short of killing Accelerator or beating him multiple times to actually put a stop to the plan. Touma beating accelerator is only a necessity as it shows a far greater disparity in data than if Misaka and Accel fought.
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