I'd guess that's the point the director is trying to make. Touma only knew about the clones' fate a little before the final showdown with Accelerator, but Mikoto has been agonized by it for a longer time. Since Index was from Touma's pov, this is an understandable difference. However, I have to say they could have shortened this arc by a couple of eps. Nevertheless, the best parts are beginning in the next episode, so it's all good at this point.
Besides, according to ANN, the director lamented this lack of light fluffy and promised such a filler arc just for you, Bill, immediately after this sisters arc finishes.