I'm OK with this type of plot, as long as everything it sorted out at the end. I hate those scenarios where you think that finally it's all going to come out right, but then in the final seconds, you realise that the bad guy is just about to destroy the vital evidence that was supposed to ensure that the true story was told and thus there is No Hope...

In this particular case, being accused of the crime was only the start because Moriarty was out to totally destroy Sherlock. However, though we have been left with a cliffhanger, I assume all will be resolved in the next series.