The qualitative explanation is that the reduction in ozone concentrations has occurred over several decades, affecting the stratospheric temperature, and the recovery (to date) has not been sufficient to compensate for the loss. As you noted, the recent ozone holes have been record-breakers. Since it's the ozone and the not the CFCs that is important, then the stratosphere is still cooling off. (Unfortunately.)
In the graph below, TLS stands for "Temperature Lower Stratosphere". This is MSU/AMSU data analyzed by Remote Sensing Systems. What I'd like to see is what the trend is after the end of the Pinatubo effect, i.e. from 1994-present. Eyeballing it on the -1.0 line makes it look pretty flat.
Another way to see it is below. I invite you to peruse the whole article -- it's nice and short, but I think it addresses the substance of the points you've raised. (They misspelled "El Chichon", by the way.) I particularly note the importance of the section entitled "Greehouse gases cause cooling higher up, too" for anyone who thinks that global warming due to anthropogenic GHG emissions to the atmosphere is not occurring.
Global warming causes stratospheric cooling
