Puella Magi Madoka Magica, or PMMM, is definitely a very interesting and well done show with plenty to say and an emotionally satisfying resolution. It is most decidedly a very dark and disturbing show that is not easy to watch and so challenges the viewer. But while PMMM may deconstruct a few tropes here and there, it is not a deconstruction of the Magical Girl genre as a whole. Before I go any further with that, I'm going to define my terms.
For a trope to be deconstructed, you have to take that trope and follow through with it without glossing over the implications of the trope that you don't want to deal with. For example, in any given Super Sentai episode there is giant robot battle in the middle of the city, yet by the start of the next episode any and all damage to the city has been undone and no one thinks anything of it, so a deconstruction of the trope would force the heroes to have to deal with the consequences one way or another; they could either have to do repair work, be hated and resented by the people they're defending, or strive to try and make sure the giant monster doesn't get into the city in the first place, things like that. What would not be a deconstruction would be adding a darker, edgier twist onto the trope; following my earlier example, making it so that every time a building gets destroyed it contributes towards the breaking of the seal on the big bad is not a deconstruction because this is not implicit to giant robot battles in the middle of a city in general. For a genre to be deconstructed, one would have to deconstruct at least half of the foundational tropes of that genre in the manner outlined above, which necessitates that those tropes be present in some form; if the tropes aren't there, then no deconstruction can take place. Finally, when I refer to the Magical Girl genre, I'm specifically referring to those stories where the magical girls are warriors fighting evil monsters preying on humanity; shows in the vein of Bewitched or the like are not a part of this discussion.
( What PMMM does and does not deconstruct and why. )
For a trope to be deconstructed, you have to take that trope and follow through with it without glossing over the implications of the trope that you don't want to deal with. For example, in any given Super Sentai episode there is giant robot battle in the middle of the city, yet by the start of the next episode any and all damage to the city has been undone and no one thinks anything of it, so a deconstruction of the trope would force the heroes to have to deal with the consequences one way or another; they could either have to do repair work, be hated and resented by the people they're defending, or strive to try and make sure the giant monster doesn't get into the city in the first place, things like that. What would not be a deconstruction would be adding a darker, edgier twist onto the trope; following my earlier example, making it so that every time a building gets destroyed it contributes towards the breaking of the seal on the big bad is not a deconstruction because this is not implicit to giant robot battles in the middle of a city in general. For a genre to be deconstructed, one would have to deconstruct at least half of the foundational tropes of that genre in the manner outlined above, which necessitates that those tropes be present in some form; if the tropes aren't there, then no deconstruction can take place. Finally, when I refer to the Magical Girl genre, I'm specifically referring to those stories where the magical girls are warriors fighting evil monsters preying on humanity; shows in the vein of Bewitched or the like are not a part of this discussion.
( What PMMM does and does not deconstruct and why. )