Stratified Sampling Variable Choice
Yes, it is very common and sometimes necessary to use the target variable for stratified sampling. 

Consider the case of fraud detection, given a bunch of features about a person (e.g. income, gender, position etc) we want to predict the likelihood of that person has committed the crime (a boolean value indicating whether the person is a suspect). This dataset is likely to be very asymmetric with very few positive examples. 

Now if we want to use k-fold cross-validation, we must stratify the samples using the target variable. If we don't, we might end up with a fold without any positive example at all and no metrics can be calculated from that fold.