I highly doubt Sherlock would let Molly out on cases, it'd be too dangerous. Well, I could see her sneaking out and, with the help of John, helping out on the case, but then she got captured, and Sherlock and Watson had to save her.
Sherlock has a broken leg or something from a previous case, so Molly helps John out in his stead. I could totally imagine Molly getting a text from Sherlock, and when John asks was Sherlock wants, she replies, "He's bored, with six 'B's, four 'O's, five 'R's, two 'E's, and one 'D'. Oh, and the husband is having an affair with the butler." "Oh, at least he's calmed down a bit."